Nucleic acid probe-based diagnostic assays targeting ssra genes of prokaryotic and eukaryotic organisms

ABSTRACT

Use of the ssrA gene or tmRNA, an RNA transcript of the ssrA gene, or fragments thereof as target regions in a nucleic acid probe assay for the detection and identification of prokaryotic and/or eukaryotic organisms is described. Nucleotide sequence alignment of tmRNA sequences from various organisms can be used to identify regions of homology and non-homology within the sequences which in turn can be used to design both genus specific and species specific oligonucleotide probes. These newly identified regions of homology and non-homology provide the basis of identifying and detecting organisms at the molecular level. Oligonucleotide probes identified in this way can be used to detect tmRNA in samples thereby giving an indication of the viability of non-viral organisms present in various sample types.

This application is a divisional application of co-pending application Ser. No. 09/959,964, filed Jan. 13, 2002, and for which priority is claimed under 35 U.S.C. §120; which is the national phase under 35 U.S.C. §371 of PCT International Application No. PCT/IE00/00066 which has an International filing date of May 15, 2000, which designated the United States of America and was published in English; which claims priority to PCT/IE99/00043, filed May 14, 1999, under 35 U.S.C. §119; the entire contents of all are hereby incorporated by reference.

TECHNICAL FIELD

This invention relates to the identification of target sequences for use in nucleic acid assays for the detection and identification of prokaryotic and/or eukaryotic organisms.

BACKGROUND ART

The ssrA gene, which encodes a small stable high copy number RNA transcript (tmRNA), is found in all bacteria and has recently been identified in chloroplasts and diatoms. It has a dual function both as a tRNA and as an mRNA molecule and is involved in rescuing truncated mRNAs which have lost stop codons, facilitating trans-translation of truncated peptides prior to protease degradation (Keiler, K. C. et al. (1996), Science, 271, 990-993). The unique function of tmRNAs has directed researchers to analyse the relationship of the secondary structure of these molecules with their function. These studies have focussed on the conservation of the secondary structure of tmRNAs from different microorganisms, and on the evolutionary significance and functional relevance of such structural conservation. Studies were carried out by Matveeva, O et al (1998), Vol. 16, No. 13, 1374-1375 to investigate oligonucleotide binding to RNA molecules using tmRNA as a model of RNA containing secondary structure. The studies did not have as their objective the identification of sites in tmRNA with the goal of designing antisense oligonucleotide for therapeutic purposes.

The number of nucleic acid targets/probes for bacterial diagnostics is currently limited. As such, the need to identify and characterise novel DNA and RNA targets for diagnostic purposes is now seen as a priority. Target nucleic acid sequences for the development of probes can be for example, plasmids, ribosomal RNA genes, intergenic regions, genes encoding virulence factors or random genomic DNA fragments. In addition, a number of RNA molecules have been described which are used as targets for RNA-based detection for example, ribosomal RNA and RNase P.

The basis of any nucleic acid-based probe assay is the requirement for well characterised nucleic acid sequences which are present in all prokaryotes and eukaryotes under study. For reliable detection of a prokaryotic or eukaryotic organism, the nucleic acid probes used should be highly specific (i.e. not cross-react with nucleic acids from other organisms) and highly sensitive (i.e. most or all strains of the organism to be detected should react with the probe). Therefore, preferred target sequences would be present in all strains of the organism concerned. Such sequences would have significant sequence variability to allow differentiation of the species concerned from other closely related species but, on the other hand, have sufficient sequence conservation to allow the detection of all strains of the species concerned. In general, the precise identification of a nucleic acid sequence, which could form the basis of a specific nucleic acid probe assay, is tedious, difficult and uncertain. To date there are few general approaches which would facilitate the development of nucleic acid probes for a wide variety of microorganisms. The nucleic acid sequences which have been identified as potentially useful targets for probe development are, for example, rRNA genes and RNA, and the rRNA 16S/23S intergenic region.

The majority of nucleic acid probe/target assays centre on the high copy number ribosomal RNAs (rRNA) and rRNA 16S/23S spacer regions (European Patent No. 0 395 292) of the bacterial cell for the purposes of detection and identification. A number of successful commercial bacterial diagnostic kits have been marketed based on these rRNA probes/targets for the detection of a variety of microrganisms. These include a range of commercial probe kits based on the 16S rRNA gene marketed by Gen-probe Inc. San Diego Calif., and DNA probes based on the 16S/23S spacer region marketed by Innogenetics N.V. Ghent, Belgium. However, many of these diagnostic kits have limitations, including lack of sensitivity due to low copy-number target sequences and lack of specificity due to sequence identity between closely related organisms in many cases.

Nucleic acid-based methods that could be applied directly to samples to give an indication of the viability of any microbes present therein would be of enormous significance for food, industrial, environmental and medical applications.

A disadvantage of DNA-based methods is that they do not distinguish between living and dead organisms. Some studies have focussed on using rRNA and mRNA as indicators of cell viability (Sheridan, G. E. C. et al. (1998) Applied and Environmental Microbiology, 64, 1313-1318). However, these sequences are not satisfactory targets as rRNA and mRNA can be present in bacterial cells up to 48 hours after cell death.

With the advent of nucleic acid based microarray-like formatting, incorporating simultaneous monitoring of multiple nucleic acid targets, there is now a clear requirement to identify and characterise novel nucleic acid sequences for use as probes and/or target regions to detect and identify viable prokaryotic and eukaryotic cells.

DISCLOSURE OF INVENTION

The invention provides use of the ssrA gene or a fragment thereof as a target region in a nucleic acid probe assay for a prokaryotic or eukaryotic organism.

Thus, the invention has application in relation to all organisms other than viruses.

No other nucleic acid probe assay has been reported which uses regions of the ssrA gene as a target region to detect and identify species of prokaryotes and eukaryotes with the attendant advantages.

According to one embodiment of the invention a fragment of the ssrA gene molecule corresponding to a region of high homology from the 5′ end of the DNA molecule can be used as a universal target region.

In an alternative embodiment of the invention a fragment of the ssrA gene molecule corresponding to a region of high homology from the 3′ end of the DNA molecule can be used as a universal target region.

In a further embodiment of the invention a fragment of the ssrA gene molecule corresponding to a region of low homology can be used as a target region in a nucleic acid probe assay to distinguish between species.

In a still further embodiment of the invention a fragment of the ssrA gene molecule corresponding to a region of low homology can be used as a target region for the generation of a genus specific probe.

As hereinafter described nucleotide sequence alignments of ssrA gene sequences from different organisms show that the 5′ and 3′ regions of these molecules demonstrate a high degree of homology and are therefore useful as universal target regions. The ssrA genes also demonstrate a more significant degree of nucleotide sequence variability between closely related organisms than any other bacterial high copy number RNA. These variable regions are ideal targets for nucleic acid assays to distinguish between species.

The invention also provides use of tmRNA, an RNA transcript of the ssrA gene, or a fragment thereof as a target region in a nucleic acid probe assay for a prokaryotic or eukaryotic organism.

According to one embodiment of this aspect of the invention a fragment of a tmRNA molecule corresponding to a region of high homology from the 5′ end of the tmRNA molecule can be used as a universal target region.

Alternatively, a fragment of a tmRNA molecule corresponding to a region of high homology from the 3′ end of the tmRNA molecule can be used as a universal target region.

According to a further embodiment of this aspect of the invention a fragment of a tmRNA molecule corresponding to a region of low homology can be used as a target region in a nucleic acid probe assay to distinguish between species.

According to a still further embodiment a fragment of a tmRNA molecule corresponding to a region of low homology can be used as a target region for the generation of a genus specific probe.

The nucleic acid probe (DNA or RNA) in accordance with the invention typically consists of at least 10 nucleotides of the ssrA gene and/or tmRNA transcript or their complementary sequence and is used in a nucleic acid probe hybridisation assay for a prokaryotic or eukaryotic organism. Probe hybridisation to its complementary sequence is typically revealed by labelling the nucleic acid probe with a radioactive or non-radioactive (e.g. colorimetric or fluorimetric) label.

In preferred embodiments said ssrA gene fragment or said tmRNA fragment can be used as the basis of a primer to be used in an amplification procedure.

Universal oligonucleotide primers directed to the 5′ and 3′ regions of either the ssrA gene or the tmRNA sequence can be used in accordance with the invention to amplify the ssrA gene or its encoding tmRNA from a wide variety of bacteria, facilitating amplification of a wide range of organisms simultaneously, whilst also enabling specific nucleic acid probe hybridisation and detection.

Preferably, the product of the amplification procedure is used as a target region in a nucleic probe assay.

Further, preferably, a cDNA transcript of a tmRNA molecule is used as a probe in a nucleic acid hybridisation assay.

Such assays can be carried out in vitro or in situ.

The target region as defined herein can be used as the basis of an assay for distinguishing between living and dead prokaryotic or eukaryotic organisms.

In contrast to rRNA and mRNA which can be present in bacterial cells following cell death, tmRNA is rapidly degraded in dead organisms. Thus, tmRNA can be a useful target for distinguishing between living and dead prokaryotic or eukaryotic organisms either directly by nucleic acid probe hybridisation to isolated bacterial RNA, or by combined RNA amplification and nucleic acid probe hybridisation to the amplified product.

Preferably, the target region is used in a multiple probe format for broad scale detection and/or identification of prokaryotic or eukaryotic organisms.

An ssrA gene probe or a tmRNA transcript probe in accordance with the invention can be linked to a microarray gene chip system for the broad scale high throughput detection and identification of prokaryotic or eukaryotic organisms.

A target region in accordance with the invention can also be used as a probe in an assay to detect prokaryotic or eukaryotic organisms in a sample of matter.

Such a sample of matter can include biological samples such as samples of tissue from the respiratory tract, the uro-genital tract or the gastrointestinal tract, or body fluids such as blood and blood fractions, sputum or cerebrospinal fluid.

An assay in accordance with the invention can also be carried out on food samples, environmental samples including air, water, marine and soil samples, and plant and animal derived samples.

According to the invention a fragment of the ssrA gene or the tmRNA transcript can also be used in an assay to obtain a DNA profile of a prokaryotic or eukaryotic organism and, thereby, distinguish between strains of the same species.

Nucleic acid sequence alignments have shown that sequence variation occurs in the ssrA gene and the tmRNA transcript within individual species. This intra-species sequence variation can be used to distinguish between strains of the same species for epidemiology, tracing of infectious agents for example, in outbreaks, or for population studies.

Other applications of the invention include the use of the ssrA gene, the tmRNA transcript or a DNA sequence complementary thereto, or a fragment thereof, to design an agent directed against infectious prokaryotic or eukaryotic organisms for therapeutic purposes.

Such agents can include antisense mRNA or oligonucleotides, ribozymes, and antagonistic peptides and are suitable for use in any kind of medical condition.

Thus, the invention can be used for the detection of viable organisms only in biological samples using the tmRNA target. Thus, during and following any anti-infectious agent drug treatment, the tmRNA target can be used to monitor the efficacy of the therapy on those specific infectious agents (e.g. antimicrobial and/or anti-parasitic treatments).

In one embodiment, the target region is used to monitor the efficacy of drug therapies against infectious agents.

In another embodiment, the target region is used to monitor the viability and level of health-promoting organisms in the gastrointestinal tract.

This aspect of the invention relates, for example, to the introduction into the gut flora of health-promoting (probiotic) organisms contained in for example yoghurt or other food to improve health. There is an interest and need to continuously monitor the presence and levels of these organisms to ensure their continued function in promoting health. The tmRNA region can be used as a target to detect viable organisms, for example in faeces, so as to monitor the presence of the health promoting organisms.

In a further embodiment, the assay is used for the quantification of prokaryotic or eukaryotic organisms.

When using probe hybridisation and/or in vitro amplification to detect organisms in a sample it is possible to determine the number of organisms present, based on the signal intensity. Real-time methods of in vitro amplification can also be used to enable the quantification of is organisms in a sample. Thus, the ability to quantify the number of organisms in a sample can be important in clinical situations for treatment purposes, for example for antibiotic or other treatments or for monitoring treatment efficacy.

A still further application of the invention is the use of a database of ssrA gene sequences to identify a prokaryotic or eukaryotic organism.

The invention provides a variety of probes for the 5′ and 3′ homologous regions and the variable regions of the ssrA gene and tmRNA sequences, the probes being derived from these sequences or sequences complementary thereto. Representative sequences are as follows:

Actinobacillus actinomycetemcomitans ssrA SEQ ID NO: 1 GGGGCTGATTCTGGATTCGACGGGATTAGCGAAGCCCGAAGT GCACGTCGAGGTGCGGTAGGCCTCGTAAATAAACCGCAAAAA AATAGTCGCAAACGACGAACAATACGCTTTAGCAGCTTAATA ACCTGCCTTTAGCCTTCGCTCCCCAGCTTCCGCTCGTAAGACG GGGATAAAGCGGAGTCAAACCAAAACGAGATCGTGTGGAAG CCACCGTTTGAGGATCGAAGCATTAAATTAAATCAAAGTAGC TTAATTGTCGCGTGTCCGTCAGCAGGATTAAGTGAATTTAAAG ACCGGACTAAACGTGTAGTGCTAACGGCAGAGGAATTTCGGA CGGGGGTTCAACTCCCCCCAGCTCCACCA Actinobacillus actinomycetemcomitans tmRNA SEQ ID NO: 2 GGGGCUGAUUCUGGAUUCGACGGGAUUAGCGAAGCCCGAAG UGCACGUCGAGGUGCGGUAGGCCUCGUAAAUAAACCGCAAA AAAAUAGUCGCAAACGACGAACAAUACGCUUUAGCAGCUUA AUAACCUGCCUUUAGCCUUCGCUCCCCAGCUUCCGCUCGUA AGACGGGGAUAAAGCGGAGUCAAACCAAAACGAGAUCGUGU GGAAGCCACCGUUUGAGGAUCGAAGCAUUAAAUUAAAUCAA AGUAGCUUAAUUGUCGCGUGUCCGUCAGCAGGAUUAAGUGA AUUUAAAGACCGGACUAAACGUGUAGUGCUAACGGCAGAGG AAUUUCGGACGGGGGUUCAACUCCCCCCAGCUCCACCA Aeromonas salmonicida ssrA, internal partial SEQ ID NO: 3 AAGATTCACGAAACCCAAGGTGCATGCCGAGGTGCGGTAGGC CTCGTTAACAAACCGCAAAAAAATAGTCGCAAACGACGAAAA CTACGCACTAGCAGCtTAATAACCTGCATAGAGCCCTTCTACC CTAGCTTGCCTGTGTCCTAGGGAATCGGAAGGTCATCCTTCAC AGGATCGTGTGGAAGTCCTGCTCGGGGCGGAAGCATTAAAAC CAATCGAGCTAGTCAATTCGTGGCGTGTCTCTCCGCAGCGGGT TGGCGAATGTAAAGAGTGACTAAGCATGTAGTACCGAGGATG TAGTAATTTTGGACGGGG Aeromonas salmonicida tmRNA, internal partial SEQ ID NO: 4 AAGAUUCACGAAACCCAAGGUGCAUGCCGAGGUGCGGUAGG CCUCGUUAACAAACCGCAAAAAAAUAGUCGCAAACGACGAA AACUACGCACUAGCAGCUUAAUAACCUGCAUAGAGCCCUUC UACCCUAGCUUGCCUGUGUCCUAGGGAAUCGGAAGGUCAUC CUUCACAGGAUCGUGUGGAAGUCCUGCUCGGGGCGGAAGCA UUAAAACCAAUCGAGCUAGUCAAUUCGUGGCGUGUCUCUCC GCAGCGGGUUGGCGAAUGUAAAGAGUGACUAAGCAUGUAGU ACCGAGGAUGUAGUAAUUUUGGACGGGG Alcaligenes eutrophus ssrA SEQ ID NO: 5 TGGGCCGACCTGGTTTCGACGTGGTTACAAAGCAGTGAGGCA TACCGAGGACCCGTCACCTCGTTAATCAATGGAATGCAATAA CTGCTAACGACGAACGTTACGCACTCGCTTAATTGCGGCCGTC CTCGCACTGGCTCGCTGACGGGCTAGGGTCGCAAGACCACGC GAGGTATTTACGTCAGATAAGCTCCGGAAGGGTCACGAAGCC GGGGACGAAAACCTAGTGACTCGCCGTCGTAGAGCGTGTTCG TCCGATGCGCCGGTTAAATCAAATGACAGAACTAAGTATGTA GAACTCTCTGTGGAGGGCTTACGGACGCGGGTTCGATTCCCGC CGGCTCCACCA Alcaligenes eutrophus tmRNA SEQ ID NO: 6 UGGGCCGACCUGGUUUCGACGUGGUUACAAAGCAGUGAGGC AUACCGAGGACCCGUCACCUCGUUAAUCAAUGGAAUGCAAU AACUGCUAACGACGAACGUUACGCACUCGCUUAAUUGCGGC CGUCCUCGCACUGGCUCGCUGACGGGCUAGGGUCGCAAGAC CACGCGAGGUAUUUACGUCAGAUAAGCUCCGGAAGGGUCAC GAAGCCGGGGACGAAAACCUAGUGACUCGCCGUCGUAGAGC GUGUUCGUCCGAUGCGCCGGUUAAAUCAAAUGACAGAACUA AGUAUGUAGAACUCUCUGUGGAGGGCUUACGGACGCGGGUU CGAUUCCCGCCGGCUCCACCA Aquifex aeolicus ssrA SEQ ID NO: 7 GGGGGCGGAAAGGATTCGACGGGGACAGGCGGTCCCCGAGG AGCAGGCCGGGTGGCTCCCGTAACAGCCGCTAAAACAGCTCC CGAAGCTGAACTCGCTCTCGCTGCCTAATTAAACGGCAGCGC GTCCCCGGTAGGTTTGCGGGTGGCCTACCGGAGGGCGTCAGA GACACCCGCTCGGGCTACTCGGTCGCACGGGGCTGAGTAGCT GACACCTAACCCGTGCTACCCTCGGGGAGCTTGCCCGTGGGC GACCCGAGGGGAAATCCTGAACACGGGCTAAGCCTGTAGAGC CTCGGATGTGGCCGCCGTCCTCGGACGCGGGTTCGATTCCCGC CGCCTCCACCA Aquifex aeolicus tmRNA SEQ ID NO: 8 GGGGGCGGAAAGGAUUCGACGGGGACAGGCGGUCCCCGAGG AGCAGGCCGGGUGGCUCCCGUAACAGCCGCUAAAACAGCUC CCGAAGCUGAACUCGCUCUCGCUGCCUAAUUAAACGGCAGC GCGUCCCCGGUAGGUUUGCGGGUGGCCUACCGGAGGGCGUC AGAGACACCCGCUCGGGCUACUCGGUCGCACGGGGCUGAGU AGCUGACACCUAACCCGUGCUACCCUCGGGGAGCUUGCCCG UGGGCGACCCGAGGGGAAAUCCUGAACACGGGCUAAGCCUG UAGAGCCUCGGAUGUGGCCGCCGUCCUCGGACGCGGGUUCG AUUCCCGCCGCCUCCACCA Bacillus megaterium ssrA, internal partial SEQ ID NO: 9 AGGGTAGTTCGAGCTTAGGTTGCGAGTCGAGGAGATGGCCTC GTTAAAACATCAACGCCAATAATAACTGGCAAATCTAACAAT AACTTCGCTTTAGCTGCATAATAGTAGCTTAGCGTTCCTCCCT CCATCGCCCATGTGGTAGGGTAAGGGACTCACTTTAAGTGGG CTACGCCGGAGTTCGCCGTCTGAGGACGAAGGAAGAGAATAA TCAGACTAGCGACTGGGACGCCTGTTGGTAGGCAGAACAGCT CGCGAATGATCAATATGCCAACTACACTCGTAGACGCTTAAGT GGCCATATTTCTGGACGTGG Bacillus megaterium tmRNA, internal partial SEQ ID NO: 10 AGGGUAGUUCGAGCUUAGGUUGCGAGUCGAGGAGAUGGCCU CGUUAAAACAUCAACGCCAAUAAUAACUGGCAAAUCUAACA AUAACUUCGCUUUAGCUGCAUAAUAGUAGCUUAGCGUUCCU CCCUCCAUCGCCCAUGUGGUAGGGUAAGGGACUCACUUUAA GUGGGCUACGCCGGAGUUCGCCGUCUGAGGACGAAGGAAGA GAAUAAUCAGACUAGCGACUGGGACGCCUGUUGGUAGGCAG AACAGCUCGCGAAUGAUCAAUAUGCCAACUACACUCGUAGA CGCUUAAGUGGCCAUAUUUCUGGACGUGG Bacillus subtilis ssrA SEQ ID NO: 11 GGGGACGTTACGGATTCGACAGGGATGGATCGAGCTTGAGCT GCGAGCCGAGAGGCGATCTCGTAAACACGCACTTAAATATAA CTGGCAAAACTAACAGTTTTAACCAAAACGTAGCATTAGCTG CCTAATAAGCGCAGCGAGCTCTTCCTGACATTGCCTATGTGTC TGTGAAGAGCACATCCAAGTAGGCTACGCTTGCGTTCCCGTCT GAGAACGTAAGAAGAGATGAACAGACTAGCTCTCGGAAGGCC CGCCCGCAGGCAAGAAGATGAGTGAAACCATAAATATGCAGG CTACGCTCGTAGACGCTTAAGTAATCGATGTTTCTGGACGTGG GTTCGACTCCCACCGTCTCCACCA Bacillus subtilis tmRNA SEQ ID NO: 12 GGGGACGUUACGGAUUCGACAGGGAUGGAUCGAGCUUGAGC UGCGAGCCGAGAGGCGAUCUCGUAAACACGCACUUAAAUAU AACUGGCAAAACUAACAGUUUUAACCAAAACGUAGCAUUAG CUGCCUAAUAAGCGCAGCGAGCUCUUCCUGACAUUGCCUAU GUGUCUGUGAAGAGCACAUCCAAGUAGGCUACGCUUGCGUU CCCGUCUGAGAACGUAAGAAGAGAUGAACAGACUAGCUCUC GGAAGGCCCGCCCGCAGGCAAGAAGAUGAGUGAAACCAUAA AUAUGCAGGCUACGCUCGUAGACGCUUAAGUAAUCGAUGUU UCUGGACGUGGGUUCGACUCCCACCGUCUCCACCA Bordetella pertussis ssrA SEQ ID NO: 13 GGGGCCGATCCGGATTCGACGTGGGTCATGAAACAGCTCAGG GCATGCCGAGCACCAGTAAGCTCGTTAATCCACTGGAACACT ACAAACGCCAACGACGAGCGTCTCGCTCTCGCCGCTTAAGCG GTGAGCCGCTGCACTGATCTGTCCTTGGGTCAGGCGGGGGAA GGCAACTTCACAGGGGGCAACCCCGAACCGCAGCAGCGACAT TCACAAGGAATCGGCCACCGCTGGGGTCACACGGCGTTGGTT TAAATTACGTGAATCGCCCTGGTCCGGCCCGTCGATCGGCTAA GTCCAGGGTTAAATCCAAATAGATCGACTAAGCATGTAGAAC TGGTTGCGGAGGGCTTGCGGACGGGGGTTCAATTCCCCCCGG CTCCACCA Bordetella pertussis tmRNA SEQ ID NO: 14 GGGGCCGAUCCGGAUUCGACGUGGGUCAUGAAACAGCUCAG GGCAUGCCGAGCACCAGUAAGCUCGUUAAUCCACUGGAACA CUACAAACGCCAACGACGAGCGUCUCGCUCUCGCCGCUUAA GCGGUGAGCCGCUGCACUGAUCUGUCCUUGGGUCAGGCGGG GGAAGGCAACUUCACAGGGGGCAACCCCGAACCGCAGCAGC GACAUUCACAAGGAAUCGGCCACCGCUGGGGUCACACGGCG UUGGUUUAAAUUACGUGAAUCGCCCUGGUCCGGCCCGUCGA UCGGCUAAGUCCAGGGUUAAAUCCAAAUAGAUCGACUAAGC AUGUAGAACUGGUUGCGGAGGGCUUGCGGACGGGGGUUCAA UUCCCCCCGGCUCCACCA Borrelia burgdorferi ssrA SEQ ID NO: 15 GGGGATGTTTTGGATTTGACTGAAAATGTTAATATTGTAAGTT GCAGGCAGAGGGAATCTCTTAAAACTTCTAAAATAAATGCAA AAAATAATAACTTTACAAGCTCAAATCTTGTAATGGCTGCTTA AGTTAGCAGAGGGTTTTGTTGAATTTGGCTTTGAGGTTCACTT ATACTCTTTTCGACATCAAAGCTTGCTTAAAAATGTTTTCAAG TTGATTTTTAGGGACTTTTATACTTGAGAGCAATTTGGTGGTTT GCTAGTATTTCCAAACCATATTGCTTAATAAAATACTAGATAA GCTTGTAGAAGCTTATAGTATTATTTTTAGGACGCGGGTTCAA TTCCCGCCATCTCCACCA Borrelia burgdorferi tmRNA SEQ ID NO: 16 GGGGAUGUUUUGGAUUUGACUGAAAAUGUUAAUAUUGUAA GUUGCAGGCAGAGGGAAUCUCUUAAAACUUCUAAAAUAAAU GCAAAAAAUAAUAACUUUACAAGCUCAAAUCUUGUAAUGGC UGCUUAAGUUAGCAGAGGGUUUUGUUGAAUUUGGCUUUGA GGUUCACUUAUACUCUUUUCGACAUCAAAGCUUGCUUAAAA AUGUUUUCAAGUUGAUUUUUAGGGACUUUUAUACUUGAGA GCAAUUUGGUGGUUUGCUAGUAUUUCCAAACCAUAUUGCUU AAUAAAAUACUAGAUAAGCUUGUAGAAGCUUAUAGUAUUA UUUUUAGGACGCGGGUUCAAUUCCCGCCAUCUCCACCA Campylobacter jejuni ssrA SEQ ID NO: 17 GGGAGCGACTTGGCTTCGACAGGAGTAAGTCTGCTTAGATGG CATGTCGCTTTGGGCAAAGCGTAAAAAGCCCAAATAAAATTA AACGCAAACAACGTTAAATTCGCTCCTGCTTACGCTAAAGCTG CGTAAGTTCAGTTGAGCCTGAAATTTAAGTCATACTATCTAGC TTAATTTTCGGTCATTTTTGATAGTGTAGCCTTGCGTTTGACAA GCGTTGAGGTGAAATAAAGTCTTAGCCTTGCTTTTGAGTTTTG GAAGATGAGCGAAGTAGGGTGAAGTAGTCATCTTTGCTAAGC ATGTAGAGGTCTTTGTGGGATTATTTTTGGACAGGGGTTCGAT TCCCCTCGCTTCCACCA Campylobacter jejuni tmRNA SEQ ID NO: 18 GGGAGCGACUUGGCUUCGACAGGAGUAAGUCUGCUUAGAUG GCAUGUCGCUUUGGGCAAAGCGUAAAAAGCCCAAAUAAAAU UAAACGCAAACAACGUUAAAUUCGCUCCUGCUUACGCUAAA GCUGCGUAAGUUCAGUUGAGCCUGAAAUUUAAGUCAUACUA UCUAGCUUAAUUUUCGGUCAUUUUUGAUAGUGUAGCCUUGC GUUUGACAAGCGUUGAGGUGAAAUAAAGUCUUAGCCUUGCU UUUGAGUUUUGGAAGAUGAGCGAAGUAGGGUGAAGUAGUC AUCUUUGCUAAGCAUGUAGAGGUCUUUGUGGGAUUAUUUU UGGACAGGGGUUCGAUUCCCCUCGCUUCCACCA Chlamydia trachomatis (D/UW-3/CX) ssrA SEQ ID NO: 19 GGGGGTGTAAAGGTTTCGACTTAGAAATGAAGCGTTAATTGC ATGCGGAGGGCGTTGGCTGGCCTCCTAAAAAGCCGACAAAAC AATAAATGCCGAACCTAAGGCTGAATGCGAAATTATCAGCTT CGCTGATCTCGAAGATCTAAGAGTAGCTGCTTAATTAGCAAA GTTGTTACCTAAATACGGGTGACCCGGTGTTCGCGAGCTCCAC CAGAGGTTTTCGAAACACCGTCATGTATCTGGTTAGAACTTAG GTCCTTTAATTCTCGAGGAAATGAGTTTGAAATTTAATGAGAG TCGTTAGTCTCTATAGGGGTTTCTAGCTGAGGAGACATAACGT ATAGTACCTAGGAACTAAGCATGTAGAGGTTAGCGGGGAGTT TACTAAGGACGAGAGTTCGACTCTCTCCACCTCCACCA Chlamydia trachomatis (D/UW-3/CX) tmRNA SEQ ID NO: 20 GGGGGUGUAAAGGUUUCGACUUAGAAAUGAAGCGUUAAUU GCAUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCGACAA AACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUCA GCUUCGCUGAUCUCGAAGAUCUAAGAGUAGCUGCUUAAUUA GCAAAGUUGUUACCUAAAUACGGGUGACCCGGUGUUCGCGA GCUCCACCAGAGGUUUUCGAAACACCGUCAUGUAUCUGGUU AGAACUUAGGUCCUUUAAUUCUCGAGGAAAUGAGUUUGAAA UUUAAUGAGAGUCGUUAGUCUCUAUAGGGGUUUCUAGCUGA GGAGACAUAACGUAUAGUACCUAGGAACUAAGCAUGUAGAG GUUAGCGGGGAGUUUACUAAGGACGAGAGUUCGACUCUCUC CACCUCCACCA Chlamydia trachomatis (mouse pneumonitis) ssrA SEQ ID NO: 21 GGGGGTGTAAAGGTTTCGACTTAGAAATGAAGCGTTAATTGC ATGCGGAGGGCGTTGGCTGGCCTCCTAAAAAGCCGACAAAAC AATAAATGCCGAACCTAAGGCTGAATGCGAAATTATCAGCTT CGCTGATCTTAATGATCTAAGAGTTGCTGCTTAATTAGCAAAG TTGTTACCTAAGTACTGGTAACCCGGTGTTCGCGAGCTCCACC AGAGGTTTTCGAAACGCCGTCATTTATCTGGTTAGAATTAGGG CCTTTTAACTCTCAAGGGAACTAATTTGAATTTTAATGAGAGT CGTTGGTCTCTATAGAGGTTTCTAGCTGAGGAGATATAACGTA AAATATTCTAGAAACTAAGCATGTAGAGGTTAGCGGGGAGTT TACTAAGGACGAGAGTTCGAATCTCTCCACCTCCACCA Chlamydia trachomatis (mouse pneumonitis) tmRNA SEQ ID NO: 22 GGGGGUGUAAAGGUUUCGACUUAGAAAUGAAGCGUUAAUU GCAUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCGACAA AACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUCA GCUUCGCUGAUCUUAAUGAUCUAAGAGUUGCUGCUUAAUUA GCAAAGUUGUUACCUAAGUACUGGUAACCCGGUGUUCGCGA GCUCCACCAGAGGUUUUCGAAACGCCGUCAUUUAUCUGGUU AGAAUUAGGGCCUUUUAACUCUCAAGGGAACUAAUUUGAAU UUUAAUGAGAGUCGUUGGUCUCUAUAGAGGUUUCUAGCUGA GGAGAUAUAACGUAAAAUAUUCUAGAAACUAAGCAUGUAG AGGUUAGCGGGGAGUUUACUAAGGACGAGAGUUCGAAUCUC UCCACCUCCACCA Chlorobium tepidum ssrA SEQ ID NO: 23 GGGGATGACAGGCTATCGACAGGATAGGTGTGAGATGTCGTT GCACTCCGAGTTTCAGCATGGACGGACTCGTTAAACAAGTCTA TGTACCAATAGATGCAGACGATTATTCGTATGCAATGGCTGCC TGATTAGCACAAGTTAATTCAGAAGCCATCGTCCTGCGGTGAA TGCGCTTACTCTGAAGCCGCCGGATGGCATAACCCGCGCTTGA GCCTACGGGTTCGCGCAAGTAAGCTCCGTACATTCATGCCCGA GGGGGTGTGCGGGTAACCAATCGGGATAAGGGGACGAACGCT GCTGGCGGTGTAATCGGACCACGAAAAACCAACCACCAGAGA TGAGTGTGGTAACTGCATCGAGCAGTGTCCTGGACGCGGGTTC AAGTCCCGCCATCTCCACCA Chlorobium tepidum tmRNA SEQ ID NO: 24 GGGGAUGACAGGCUAUCGACAGGAUAGGUGUGAGAUGUCGU UGCACUCCGAGUUUCAGCAUGGACGGACUCGUUAAACAAGU CUAUGUACCAAUAGAUGCAGACGAUUAUUCGUAUGCAAUGG CUGCCUGAUUAGCACAAGUUAAUUCAGAAGCCAUCGUCCUG CGGUGAAUGCGCUUACUCUGAAGCCGCCGGAUGGCAUAACC CGCGCUUGAGCCUACGGGUUCGCGCAAGUAAGCUCCGUACA UUCAUGCCCGAGGGGGUGUGCGGGUAACCAAUCGGGAUAAG GGGACGAACGCUGCUGGCGGUGUAAUCGGACCACGAAAAAC CAACCACCAGAGAUGAGUGUGGUAACUGCAUCGAGCAGUGU CCUGGACGCGGGUUCAAGUCCCGCCAUCUCCACCA Cyanophora paradoxa (alga) cyanelle ssrA SEQ ID NO: 25 GGGGCTGTTTAGGTTTCGACGTTTTTTTCTAATTATGTTTGTTA AGCAAGTCGAGGATTTGTTCTATCTCGAAAATCAAGAACTCTC AAAATTTAAACGCAACTAATATTGTACGTTTTAACCGTAAAGC AGCTTTCGCTGTTTAATAATTACTTTTAATTTAAAAACCTAATT TTTTTAGGAATTTATTTATTTATTGTTTATCCTGCTTAATGAAT TAAAAAAAGCTATACTTGTGAATAAACGCATAATTTAAAAAA ACGGACGTGGGTTCAAATCCCACCAGCTCCACCA Cyanophora paradoxa (alga) cyanelle tmRNA SEQ ID NO: 26 GGGGCUGUUUAGGUUUCGACGUUUUUUUCUAAUUAUGUUU GUUAAGCAAGUCGAGGAUUUGUUCUAUCUCGAAAAUCAAGA ACUCUCAAAAUUUAAACGCAACUAAUAUUGUACGUUUUAAC CGUAAAGCAGCUUUCGCUGUUUAAUAAUUACUUUUAAUUUA AAAACCUAAUUUUUUUAGGAAUUUAUUUAUUUAUUGUUUA UCCUGCUUAAUGAAUUAAAAAAAGCUAUACUUGUGAAUAAA CGCAUAAUUUAAAAAAACGGACGUGGGUUCAAAUCCCACCA GCUCCACCA Clostridium acetobutylicum ssrA, 3′ partial SEQ ID NO: 27 AATCTGGCGTCGAGAGCGGGGAAACGAGCCTTACAAAGCTTT GAGTAAGGAACGGAATTTATGAAGCTACTGAAGTGAAAAGCT TGTTTGTAGGCGTTTCATGGAGGGAATGTTAAAATACAAACTG CACTCGGAGATGCTTAATGAAACCATTTTCGGACAGGGGTTCG ATTCCCCTCGCCTCCACCA Clostridium acetobutylicum tmRNA, 3′ partial SEQ ID NO: 28 AAUCUGGCGUCGAGAGCGGGGAAACGAGCCUUACAAAGCUU UGAGUAAGGAACGGAAUUUAUGAAGCUACUGAAGUGAAAA GCUUGUUUGUAGGCGUUUCAUGGAGGGAAUGUUAAAAUAC AAACUGCACUCGGAGAUGCUUAAUGAAACCAUUUUCGGACA GGGGUUCGAUUCCCCUCGCCUCCACCA Deinococcus radiodurans ssrA SEQ ID NO: 29 GGGGGTGACCCGGTTTCGACAGGGGAACTGAAGGTGATGTTG CGTGTCGAGGTGCCGTTGGCCTCGTAAACAAACGGCAAAGCC ATTTAACTGGCAACCAGAACTACGCTCTCGCTGCTTAAGTGAG ATGACGACCGTGCAGCCCGGCCTTTGGCGTCGCGGAAGTCAC TAAAAAAGAAGGCTAGCCCAGGCGATTCTCCATAGCCGACGG CGAAACTTTATGGAGCTACGGCCTGCGAGAACCTGCCCACTG GTGAGCGCCGGCCCGACAATCAAACAGTGGGATACACACGTA GACGCACGCTGGACGGACCTTTGGACGGCGGTTCGACTCCGC CCACCTCCACCA Deinococcus radiodurans tmRNA SEQ ID NO: 30 GGGGGUGACCCGGUUUCGACAGGGGAACUGAAGGUGAUGUU GCGUGUCGAGGUGCCGUUGGCCUCGUAAACAAACGGCAAAG CCAUUUAACUGGCAACCAGAACUACGCUCUCGCUGCUUAAG UGAGAUGACGACCGUGCAGCCCGGCCUUUGGCGUCGCGGAA GUCACUAAAAAAGAAGGCUAGCCCAGGCGAUUCUCCAUAGC CGACGGCGAAACUUUAUGGAGCUACGGCCUGCGAGAACCUG CCCACUGGUGAGCGCCGGCCCGACAAUCAAACAGUGGGAUA CACACGUAGACGCACGCUGGACGGACCUUUGGACGGCGGUU CGACUCCGCCCACCUCCACCA Desulfovibrio desulfuricans ssrA, internal partial SEQ ID NO: 31 GGGACTGGAACCGTAGCGGCAGGTCGAGGCGCCGCTGGCCTC GTAAAAAGCGGCACAAAAGTAATTGCCAACAACGATTACGAC TACGCTTACGCTGCCTAATAACAGCGAGGCAATGACCGTTTAA CGGTCGCGCCGATCAGGGCCATGCCTGATAACCCTGATTGGC GACACTTATCAGGCTGGCGAAAACCGGCTCTCGCCGGGGTTTT TCGCGAGGAGTTTACCGGCGGGATTGCTGCGTTGTGCCTGGTC AGGGGCCAACAGCGCGGTGAAATACATACTTGACCTAAACCT GTAATGCTTCGTGTGGAATGTTCTCGGACGGGG Desulfovibrio desulfuricans tmRNA, internal partial SEQ ID NO: 32 GGGACUGGAACCGUAGCGGCAGGUCGAGGCGCCGCUGGCCU CGUAAAAAGCGGCACAAAAGUAAUUGCCAACAACGAUUACG ACUACGCUUACGCUGCCUAAUAACAGCGAGGCAAUGACCGU UUAACGGUCGCGCCGAUCAGGGCCAUGCCUGAUAACCCUGA UUGGCGACACUUAUCAGGCUGGCGAAAACCGGCUCUCGCCG GGGUUUUUCGCGAGGAGUUUACCGGCGGGAUUGCUGCGUUG UGCCUGGUCAGGGGCCAACAGCGCGGUGAAAUACAUACUUG ACCUAAACCUGUAAUGCUUCGUGUGGAAUGUUCUCGGACGG GG Dichelobacter nodosus ssrA, 3′ partial SEQ ID NO: 33 CTCGAGGTGCATGTCGAGAATGAGAGAATCTCGTTAAATACTT TCAAAACTTATAGTTGCAAACGACGACAACTACGCTTTAGCG GCTTAATTCCCGCTTTCGCTTACCTAGATTTGTCTGTGGGTTTA CCGTAAGCGACATTAACACAGAATCGCTGGTTAACGCGTCCG CTGTTAATCGGTTAAATTAAGCGGAATCGCTTGTAAAATGCCT GAGCGTTGGCTGTTTATGAGTTAAACCTAATTAACTGCTCTAA ACATGTAGTACCAAAAGTTAAGGATTCGCGGACGGGGGTTCA AATCCCCCCGCCTCCACCA Dichelobacter nodosus tmRNA, 3′ partial SEQ ID NO: 34 CUCGAGGUGCAUGUCGAGAAUGAGAGAAUCUCGUUAAAUAC UUUCAAAACUUAUAGUUGCAAACGACGACAACUACGCUUUA GCGGCUUAAUUCCCGCUUUCGCUUACCUAGAUUUGUCUGUG GGUUUACCGUAAGCGACAUUAACACAGAAUCGCUGGUUAAC GCGUCCGCUGUUAAUCGGUUAAAUUAAGCGGAAUCGCUUGU AAAAUGCCUGAGCGUUGGCUGUUUAUGAGUUAAACCUAAUU AACUGCUCUAAACAUGUAGUACCAAAAGUUAAGGAUUCGCG GACGGGGGUUCAAAUCCCCCCGCCUCCACCA Enterococcus faecalis ssrA SEQ ID NO: 35 GGGGGCGTTACGGATTCGACAGGCATAGTTGAGCTTGAATTG CGTTTCGTAGGTTACGGCTACGTTAAAACGTTACAGTTAAATA TAACTGCTAAAAACGAAAACAATTCTTTCGCTTTAGCTGCCTA AAAACCAGCTAGCGAAGATCCTCCCGGCATCGCCCATGTGCT CGGGTCAGGGTCCTAATCGAAGTGGGATACGCTAAATTTTTCC GTCTGTAAAATTTAGAGGAGCTTACCAGACTAGCAATACAGA ATGCCTGTCACTCGGCACGCTGTAAAGCGAACCTTTAAATGAG TGTCTATGAACGTAGAGATTTAAGTGGCAATATGTTTGGACGC GGGTTCGACTCCCGCCGTCTCCACCA Enterococcus faecalis tmRNA SEQ ID NO: 36 GGGGGCGUUACGGAUUCGACAGGCAUAGUUGAGCUUGAAUU GCGUUUCGUAGGUUACGGCUACGUUAAAACGUUACAGUUAA AUAUAACUGCUAAAAACGAAAACAAUUCUUUCGCUUUAGCU GCCUAAAAACCAGCUAGCGAAGAUCCUCCCGGCAUCGCCCA UGUGCUCGGGUCAGGGUCCUAAUCGAAGUGGGAUACGCUAA AUUUUUCCGUCUGUAAAAUUUAGAGGAGCUUACCAGACUAG CAAUACAGAAUGCCUGUCACUCGGCACGCUGUAAAGCGAAC CUUUAAAUGAGUGUCUAUGAACGUAGAGAUUUAAGUGGCA AUAUGUUUGGACGCGGGUUCGACUCCCGCCGUCUCCACCA Escherichia coli ssrA SEQ ID NO: 37 GGGGCTGATTCTGGATTCGACGGGATTTGCGAAACCCAAGGT GCATGCCGAGGGGCGGTTGGCCTCGTAAAAAGCCGCAAAAAA TAGTCGCAAACGACGAAAACTACGCTTTAGCAGCTTAATAAC CTGCTTAGAGCCCTCTCTCCCTAGCCTCCGCTCTTAGGACGGG GATCAAGAGAGGTCAAACCCAAAAGAGATCGCGTGGAAGCCC TGCCTGGGGTTGAAGCGTTAAAACTTAATCAGGCTAGTTTGTT AGTGGCGTGTCCGTCCGCAGCTGGCAAGCGAATGTAAAGACT GACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGCG GGTTCAACTCCCGCCAGCTCCACCA Escherichia coli tmRNA SEQ ID NO: 38 GGGGCUGAUUCUGGAUUCGACGGGAUUUGCGAAACCCAAGG UGCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAA AAUAGUCGCAAACGACGAAAACUACGCUUUAGCAGCUUAAU AACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGG ACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCGCGUGG AAGCCCUGCCUGGGGUUGAAGCGUUAAAACUUAAUCAGGCU AGUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAU GUAAAGACUGACUAAGCAUGUAGUACCGAGGAUGUAGGAAU UUCGGACGCGGGUUCAACUCCCGCCAGCUCCACCA Haemophilus influenzae ssrA SEQ ID NO: 39 GGGGCTGATTCTGGATTCGACGGGATTAGCGAAGCCCAAGGT GCACGTCGAGGTGCGGTAGGCCTCGTAAATAAACCGCAAAAA AATAGTCGCAAACGACGAACAATACGCTTTAGCAGCTTAATA ACCTGCATTTAGCCTTCGCGCTCCAGCTTCCGCTCGTAAGACG GGGATAACGCGGAGTCAAACCAAAACGAGATCGTGTGGAAGC CACCGTTTGAGGATCGAAGCACTAAATTGAATCAAACTAGCTT AAGTTTAGCGTGTCTGTCCGCATGCTTAAGTGAAATTAAAGAC GAGACTAAACGTGTAGTACTGAAGGTAGAGTAATTTCGGACG GGGGTTCAACTCCCCCCAGCTCCACCA Haemophilus influenzae tmRNA SEQ ID NO: 40 GGGGCUGAUUCUGGAUUCGACGGGAUUAGCGAAGCCCAAGG UGCACGUCGAGGUGCGGUAGGCCUCGUAAAUAAACCGCAAA AAAAUAGUCGCAAACGACGAACAAUACGCUUUAGCAGCUUA AUAACCUGCAUUUAGCCUUCGCGCUCCAGCUUCCGCUCGUA AGACGGGGAUAACGCGGAGUCAAACCAAAACGAGAUCGUGU GGAAGCCACCGUUUGAGGAUCGAAGCACUAAAUUGAAUCAA ACUAGCUUAAGUUUAGCGUGUCUGUCCGCAUGCUUAAGUGA AAUUAAAGACGAGACUAAACGUGUAGUACUGAAGGUAGAG UAAUUUCGGACGGGGGUUCAACUCCCCCCAGCUCCACCA Helicobacter pylori (ATCC 43504) ssrA, internal partial SEQ ID NO: 41 AGATTTCTTGTCGCGCAGATAGCATGCCAAGCGCTGCTTGTAA AACAGCAACAAAAATAACTGTAAACAACACAGATTACGCTCC AGCTTACGCTAAAGCTGCGTGAGTTAATCTCCTTTTGGAGCTG GACTGATTAGAATTTCTAGCGTTTTAATCGCTCCATAACCTTA AGCTAGACGCTTTTAAAAGGTGGTTCGCCTTTTAAACTAAGAA ACAAGAACTCTTGAAACTATCTTAAGGTTTTAGAAAGTTGGAC CAGAGCTAGTTTTAAGGCTAAAAACTAACCAATTTTCTAAGCA TTGTAGAAGTTTGTGTTTAGGGCAAGATTTTTGGACTGGG Helicobacter pylori (ATCC 43504) tmRNA, internal partial SEQ ID NO: 42 AGAUUUCUUGUCGCGCAGAUAGCAUGCCAAGCGCUGCUUGU AAAACAGCAACAAAAAUAACUGUAAACAACACAGAUUACGC UCCAGCUUACGCUAAAGCUGCGUGAGUUAAUCUCCUUUUGG AGCUGGACUGAUUAGAAUUUCUAGCGUUUUAAUCGCUCCAU AACCUUAAGCUAGACGCUUUUAAAAGGUGGUUCGCCUUUUA AACUAAGAAACAAGAACUCUUGAAACUAUCUUAAGGUUUUA GAAAGUUGGACCAGAGCUAGUUUUAAGGCUAAAAACUAACC AAUUUUCUAAGCAUUGUAGAAGUUUGUGUUUAGGGCAAGA UUUUUGGACUGGG Helicobacter pylori (strain 26695) ssrA SEQ ID NO: 43 GGGGCTGACTTGGATTTCGACAGATTTCTTGTCGCACAGATAG CATGCCAAGCGCTGCTTGTAAAACAGCAACAAAAATAACTGT AAACAACACAGATTACGCTCCAGCTTACGCTAAAGCTGCGTG AGTTAATCTCCTTTTGGAGCTGGACTGATTAGAATTTCTAGCG TTTTAATCGCTCCATAACCTTAAGCTAGACGCTTTTAAAAGGT GGTTCGCCTTTTAAACTAAGAAACAAGAACTCTTGAAACTATC TCAAGGTTTTAGAAAGTTGGACCAGAGCTAGTTTTAAGGCTAA AAAACCAACCAATTTTCTAAGCATTGTAGAAGTTTGTGTTTAG GGCAAGATTTTTGGACTGGGGTTCGATTCCCCACAGCTCCACCA Helicobacter pylori (strain 26695) tmRNA SEQ ID NO: 44 GGGGCUGACUUGGAUUUCGACAGAUUUCUUGUCGCACAGAU AGCAUGCCAAGCGCUGCUUGUAAAACAGCAACAAAAAUAAC UGUAAACAACACAGAUUACGCUCCAGCUUACGCUAAAGCUG CGUGAGUUAAUCUCCUUUUGGAGCUGGACUGAUUAGAAUUU CUAGCGUUUUAAUCGCUCCAUAACCUUAAGCUAGACGCUUU UAAAAGGUGGUUCGCCUUUUAAACUAAGAAACAAGAACUCU UGAAACUAUCUCAAGGUUUUAGAAAGUUGGACCAGAGCUAG UUUUAAGGCUAAAAAACCAACCAAUUUUCUAAGCAUUGUAG AAGUUUGUGUUUAGGGCAAGAUUUUUGGACUGGGGUUCGA UUCCCCACAGCUCCACCA Klebsiella aerogenes (NCTC 9528)ssrA, internal partial SEQ ID NO: 45 GGGATTCGCGAAACCCAAGGTGCATGCCGAGGGGCGGTTGGC CTCGTAAAAAGCCGCAAAAAAATAGTCGCAAACGACGAAAAC TACGCTTTAGCAGCTTAATAACCTGCTAAGAGCCCTCTCTCCC TAGCTTCCGCTCCTAAGACGGGGAATAAAGAGAGGTCAAACC CAAAAGAGATCGCGTGGAAGCCCTGCCTGGGGTTGAAGCGTT AAAACTAATCAGGCTAGTTTGTCAGTGGCGTGTCCGTCCGCAG CTGGCCAGCGAATGTAAAGACTGGACTAAGCATGTAGTGCCG AGGATGTAGGAATTTC Klebsiella aerogenes (NCTC 9528) tmRNA, internal partial SEQ ID NO: 46 GGGAUUCGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUUGG CCUCGUAAAAAGCCGCAAAAAAAUAGUCGCAAACGACGAAA ACUACGCUUUAGCAGCUUAAUAACCUGCUAAGAGCCCUCUC UCCCUAGCUUCCGCUCCUAAGACGGGGAAUAAAGAGAGGUC AAACCCAAAAGAGAUCGCGUGGAAGCCCUGCCUGGGGUUGA AGCGUUAAAACUAAUCAGGCUAGUUUGUCAGUGGCGUGUCC GUCCGCAGCUGGCCAGCGAAUGUAAAGACUGGACUAAGCAU GUAGUGCCGAGGAUGUAGGAAUUUC Lactobacillus lactis (NCTC 662)ssrA, internal partial SEQ ID NO: 47 AAGCACAGTTCGAGCTTGAATTGCGTTTCGTAGGTTACGTCTA CGTTAAAACGTTACAGTTAAATATAACTGCTAAAAACGAAAA CAACTCTTACGCTTTAGCTGCCTAAAAACAGTTAGCGTAGATC CTCTCGGCATCGCCCATGTGCTCGAGTAAGGGTCTCAAATTTA GTGGGATACGTTAAACTTTTCCGTCTGTAAAGTTTAAAAGAGA TCATCAGACTAGCGATACAGAATGCCTGTCACTCGGCAAGCT GTAAAGCGAAACCTCAAATGAGTTGACTATGAACGTAGATTT TTAAGTGTCGATGTGTTT Lactobacillus lactis (NCTC 662) tmRNA, internal partial SEQ ID NO: 48 AAGCACAGUUCGAGCUUGAAUUGCGUUUCGUAGGUUACGUC UACGUUAAAACGUUACAGUUAAAUAUAACUGCUAAAAACGA AAACAACUCUUACGCUUUAGCUGCCUAAAAACAGUUAGCGU AGAUCCUCUCGGCAUCGCCCAUGUGCUCGAGUAAGGGUCUC AAAUUUAGUGGGAUACGUUAAACUUUUCCGUCUGUAAAGUU UAAAAGAGAUCAUCAGACUAGCGAUACAGAAUGCCUGUCAC UCGGCAAGCUGUAAAGCGAAACCUCAAAUGAGUUGACUAUG AACGUAGAUUUUUAAGUGUCGAUGUGUUU Legionella pneumophila ssrA, internal partial SEQ ID NO: 49 GTGGGTTGCAAAACCGGAAGTGCATGCCGAGAAGGAGATCTC TCGTAAATAAGACTCAATTAAATATAAATGCAAACGATGAAA ACTTTGCTGGTGGGGAAGCTATCGCTGCCTAATAAGCACTTTA GTTAAACCATCACTGTGTACTGGCCAATAAACCCAGTATCCCG TTCGACCGAGCCCGCTTATCGGTATCGAATCAACGGTCATAAG AGATAAGCTAGCGTCCTAATCTATCCCGGGTTATGGCGCGAA ACTCAGGGAATCGCTGTGTATCATCCTGCCCGTCGGAGGAGCC ACAGTTAAATTCAAAAGACAAGGCTATGCATGTAGAGCTAAA GGCAGAGGACTTGCGGACGCGG Legionella pneumophila tmRNA, internal partial SEQ ID NO: 50 GUGGGUUGCAAAACCGGAAGUGCAUGCCGAGAAGGAGAUCU CUCGUAAAUAAGACUCAAUUAAAUAUAAAUGCAAACGAUGA AAACUUUGCUGGUGGGGAAGCUAUCGCUGCCUAAUAAGCAC UUUAGUUAAACCAUCACUGUGUACUGGCCAAUAAACCCAGU AUCCCGUUCGACCGAGCCCGCUUAUCGGUAUCGAAUCAACG GUCAUAAGAGAUAAGCUAGCGUCCUAAUCUAUCCCGGGUUA UGGCGCGAAACUCAGGGAAUCGCUGUGUAUCAUCCUGCCCG UCGGAGGAGCCACAGUUAAAUUCAAAAGACAAGGCUAUGCA UGUAGAGCUAAAGGCAGAGGACUUGCGGACGCGG Listeria grayi ssrA, internal partial SEQ ID NO: 51 ACAGGGATAGGTCGAGCTTGAGTTGCGAGCCGGGGGGATCGG CCCGTCATCAACGTCAAAGCCAATAATAACTGGCAAACAAAA CAACAATTTAGCTTTCGCTGCCTAATAGCAGTCTGAATAGCTG ATCCTCCGTGCATCACCCATGTGCTACGGTAAGGGTCTCACTT TTAAGTGGGTTACGCTGGCTTATCTCCGTCTGGGGCAAACGAG AAGAGCATAATCAGACTAGCTAGATAGAGCCCTGACGCCGGG CAGACATCTATGCGAAATCCAAATACGGCAACTACGCTCGTA GATGCTCAAGTGCCGATATTTCTGG Listeria grayi tmRNA, internal partial SEQ ID NO: 52 ACAGGGAUAGGUCGAGCUUGAGUUGCGAGCCGGGGGGAUCG GCCCGUCAUCAACGUCAAAGCCAAUAAUAACUGGCAAACAA AACAACAAUUUAGCUUUCGCUGCCUAAUAGCAGUCUGAAUA GCUGAUCCUCCGUGCAUCACCCAUGUGCUACGGUAAGGGUC UCACUUUUAAGUGGGUUACGCUGGCUUAUCUCCGUCUGGGG CAAACGAGAAGAGCAUAAUCAGACUAGCUAGAUAGAGCCCU GACGCCGGGCAGACAUCUAUGCGAAAUCCAAAUACGGCAAC UACGCUCGUAGAUGCUCAAGUGCCGAUAUUUCUGG Listeria innocua ssrA, internal partial SEQ ID NO: 53 ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGT CCTCGTTATCAACGTCAAAGCCAATAATAACTGGCAAAGAAA AACAAAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCT GATCCTCCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACT CTAAGTGGGCTACACTAGTTAATCTCCGTCTGAGGTTAAATAG AAGAGCTTAATCAGACTAGCTGAATGGAAGCCTGTTACCGGG CTGATGTTTATGCGAAATGCTAATACGGTGACTACGCTCGTAG ATATTCAAGTGCCGATATTTCTGG Listeria innocua tmRNA, internal partial SEQ ID NO: 54 ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCG UCCUCGUUAUCAACGUCAAAGCCAAUAAUAACUGGCAAAGA AAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAU AGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGU CUCACUCUAAGUGGGCUACACUAGUUAAUCUCCGUCUGAGG UUAAAUAGAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCU GUUACCGGGCUGAUGUUUAUGCGAAAUGCUAAUACGGUGAC UACGCUCGUAGAUAUUCAAGUGCCGAUAUUUCUGG Listeria monocytogenes (NCTC 7973)ssrA, internal partial SEQ ID NO: 55 ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGT CCTCGTTATCAACGTCAAAGCCAATAATAACTGGCAAAGAAA AACAAAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCT GATCCTCCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACT CTAAGTGGGCTACACTAGTTAATCTCCGTCTGGGGTTAAATAG AAGAGCTTAATCAGACTAGCTGAATGGAAGCCTGTTACCGGG CCGATGTTTATGCGAAATGCTAATACGGTGACTACGCTCGTAG ATATTTAAGTGCCGATATTTCTGG Listeria monocytogenes (NCTC 7973)tmRNA, internal partial SEQ ID NO: 56 ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCG UCCUCGUUAUCAACGUCAAAGCCAAUAAUAACUGGCAAAGA AAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAU AGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGU CUCACUCUAAGUGGGCUACACUAGUUAAUCUCCGUCUGGGG UUAAAUAGAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCU GUUACCGGGCCGAUGUUUAUGCGAAAUGCUAAUACGGUGAC UACGCUCGUAGAUAUUUAAGUGCCGAUAUUUCUGG Listeria monocytogenes (NCTC 11994) ssrA, internal partial SEQ ID NO: 57 CAAAGCCAATAATAACTGGCAAAGAAAAACAAAACCTAGCTT TCGCTGCCTAATAAGCAGTAGCATAGCTGATCCTCCGTGCATC GCCCATGTGCTACGGTAAGGGTCTCACTCTAAGTGGGCTACAC TAGTTAATCTCCGTCTGGGGTTAAATAGAAGAGCTTAATCAGA CTAGCTGAATGGAAGCCTGTTACCGGGCCGATGTTTATGCGAA ATGCTAATACGGTGACTACGCTCGTAGATATTT Listeria monocytogenes (NCTC 11994) tmRNA, internal partial SEQ ID NO: 58 CAAAGCCAAUAAUAACUGGCAAAGAAAAACAAAACCUAGCU UUCGCUGCCUAAUAAGCAGUAGCAUAGCUGAUCCUCCGUGC AUCGCCCAUGUGCUACGGUAAGGGUCUCACUCUAAGUGGGC UACACUAGUUAAUCUCCGUCUGGGGUUAAAUAGAAGAGCUU AAUCAGACUAGCUGAAUGGAAGCCUGUUACCGGGCCGAUGU UUAUGCGAAAUGCUAAUACGGUGACUACGCUCGUAGAUAUUU Listeria murrayi ssrA, internal partial SEQ ID NO: 59 ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGT CCTCGTTATCAACGTCAAAGCCAATAATAACTGGCAAAGAAA AACAAAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCT GATCCTCCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACT CTAAGTGGGCTACACTAGTTAATCTCCGTCTGAGGTTAAATAG AAGAGCTTAATGAGACTAGCTGAATGGAAGCCTGTTACCGGG CTGATGTTTATGCGAAATGCTAATACGGTGACTACGCTCGTAG ATATTCAAGTGCCGATATTTCTGG Listeria murrayi tmRNA, internal partial SEQ ID NO: 60 ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCG UCCUCGUUAUCAACGUCAAAGCCAAUAAUAACUGGCAAAGA AAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAU AGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGU CUCACUCUAAGUGGGCUACACUAGUUAAUCUCCGUCUGAGG UUAAAUAGAAGAGCUUAAUGAGACUAGCUGAAUGGAAGCCU GUUACCGGGCUGAUGUUUAUGCGAAAUGCUAAUACGGUGAC UACGCUCGUAGAUAUUCAAGUGCCGAUAUUUCUGG Listeria welshimeri ssrA, internal partial SEQ ID NO: 61 ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGT CCTCGTTATCAACGTCAAAGCCAATAATAACTGGCAAAGAAA AACAAAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCT GATCCTCCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACT CTAAGTGGGCTACACTGGCTAATCTCCGTCTGAGGTTAGTTGG AAGAGCTTAATCAGACTAGCTGAATGGAAGCCTGTTACCGGG CCGATGTTTATGCGAAATGCTAATACGGTGACTACGCTCGTAG ATATTTAAGTGCCGATATTTCTGG Listeria welshimeri tmRNA, internal partial SEQ ID NO: 62 ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCG UCCUCGUUAUCAACGUCAAAGCCAAUAAUAACUGGCAAAGA AAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAU AGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGU CUCACUCUAAGUGGGCUACACUGGCUAAUCUCCGUCUGAGG UUAGUUGGAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCU GUUACCGGGCCGAUGUUUAUGCGAAAUGCUAAUACGGUGAC UACGCUCGUAGAUAUUUAAGUGCCGAUAUUUCUGG Marinobacter hydrocarbonoclasticus ssrA, internal partial SEQ ID NO: 63 GCCGGTGACGAACCCTTGGGTGCATGCCGAGATGGCAGCGAA TCTCGTAAATCCAAAGCTGCAACGTAATAGTCGCAAACGACG AAAACTACGCACTGGCGGCGTAAGCCGTTCCAGTCGTCCTGG CTGAGGCGCCTATAACTCAGTAGCAACATCCCAGGACGTCAT CGCTTATAGGCTGCTCCGTTCACCAGAGCTCACTGGTGTTCGG CTAAGATTAAAGAGCTCGCCTCTTGCACCCTGACCTTCGGGTC GCTTGAGGTTAAATCAATAGAAGGACACTAAGCATGTAGACC TCAAGGCCTAGTGCTGGCGGACGCGG Marinobacter hydrocarbonoclasticus tmRNA, internal partial SEQ ID NO: 64 GCCGGUGACGAACCCUUGGGUGCAUGCCGAGAUGGCAGCGA AUCUCGUAAAUCCAAAGCUGCAACGUAAUAGUCGCAAACGA CGAAAACUACGCACUGGCGGCGUAAGCCGUUCCAGUCGUCC UGGCUGAGGCGCCUAUAACUCAGUAGCAACAUCCCAGGACG UCAUCGCUUAUAGGCUGCUCCGUUCACCAGAGCUCACUGGU GUUCGGCUAAGAUUAAAGAGCUCGCCUCUUGCACCCUGACC UUCGGGUCGCUUGAGGUUAAAUCAAUAGAAGGACACUAAGC AUGUAGACCUCAAGGCCUAGUGCUGGCGGACGCGG Mycobacterium avium ssrA, internal partial SEQ ID NO: 65 TTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAACT GACCACCGTAAGCGTCGTTGCAAATAGATAAGCGCCGATTCA CATCAGCGCGACTTACCTCTCGCTGCCTAAGCGACAGCTAGTC CGTCAGCCCGGGAACGCCCTCGACCCGGAGCCTGGCGTCAGC TAGAGGGATCCACCGATGAGTTCGGTCGCGGGACTCATCGGG ACACCAACAGCGACTGGGATCGTCATCCTGGCTTGTTCGCGTG ACCAGGAGATCCGAGTAGAGGCATAGCGAACTGCGCACGGAG AAGCCTTGAGGGAATGCCGTAGAACCCGGGTTCGATTCCCAA Mycobacterium avium tmRNA, internal partial SEQ ID NO: 66 UUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAC UGACCACCGUAAGCGUCGUUGCAAAUAGAUAAGCGCCGAUU CACAUCAGCGCGACUUACCUCUCGCUGCCUAAGCGACAGCU AGUCCGUCAGCCCGGGAACGCCCUCGACCCGGAGCCUGGCG UCAGCUAGAGGGAUCCACCGAUGAGUUCGGUCGCGGGACUC AUCGGGACACCAACAGCGACUGGGAUCGUCAUCCUGGCUUG UUCGCGUGACCAGGAGAUCCGAGUAGAGGCAUAGCGAACUG CGCACGGAGAAGCCUUGAGGGAAUGCCGUAGAACCCGGGUU CGAUUCCCAA Mycobacterium bovis ssrA, internal partial SEQ ID NO: 67 TTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAAGA GACCACCGTAAGCGTCGTTGCGACCAAATAAGCGCCGATTCA CATCAGCGCGACTACGTCTCGCTGCCTAAGCGACGGCTAGTCT GTCAGACCGGGAACGCCCTCGGCCCGGACCCTGGCATCAGCT AGAGGGATCCACCGATGAGTCCGGTCGCGGGACTCCTCGGGA CAACCACAGCGACTGGGATCGTCATCTCGGCTAGTTCGCGTGA CCGGGAGATCCGAGCAGAGGCATAGCGAACTGCGCACGGAG AAGCCTTGAGGGAATGCCGTAGG Mycobacterium bovis tmRNA, internal partial SEQ ID NO: 68 UUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAG AGACCACCGUAAGCGUCGUUGCGACCAAAUAAGCGCCGAUU CACAUCAGCGCGACUACGUCUCGCUGCCUAAGCGACGGCUA GUCUGUCAGACCGGGAACGCCCUCGGCCCGGACCCUGGCAU CAGCUAGAGGGAUCCACCGAUGAGUCCGGUCGCGGGACUCC UCGGGACAACCACAGCGACUGGGAUCGUCAUCUCGGCUAGU UCGCGUGACCGGGAGAUCCGAGCAGAGGCAUAGCGAACUGC GCACGGAGAAGCCUUGAGGGAAUGCCGUAGG Mycobacterium leprae ssrA SEQ ID NO: 69 GGGGCTGAAAGGTTTCGACTTCGCGCATCGAATCAAGGGAAG CGTGCCGGTGCAGGCAAGAGACCACCGTAAGCGTCGTTGCAG CAATATAAGCGCCGATTCATATCAGCGCGACTATGCTCTCGCT GCCTAAGCGATGGCTAGTCTGTCAGACCGGGAACGCCCTCGT CCCGGAGCCTGGCATCAGCTAGAGGGATCTACCGATGGGTTC GGTCGCGGGACTCGTCGGGACACCAACCGCGACTGGGATCGT CATCCTGGCTAGTTCGCGTGATCAGGAGATCCGAGTAGAGGC ATAGCGAACTACGCACGGAGAAGCCTTGAGGGAAATGCCGTA GGACCCGGGTTCGATTCCCGGCAGCTCCACCA Mycobacterium leprae tmRNA SEQ ID NO: 70 GGGGCUGAAAGGUUUCGACUUCGCGCAUCGAAUCAAGGGAA GCGUGCCGGUGCAGGCAAGAGACCACCGUAAGCGUCGUUGC AGCAAUAUAAGCGCCGAUUCAUAUCAGCGCGACUAUGCUCU CGCUGCCUAAGCGAUGGCUAGUCUGUCAGACCGGGAACGCC CUCGUCCCGGAGCCUGGCAUCAGCUAGAGGGAUCUACCGAU GGGUUCGGUCGCGGGACUCGUCGGGACACCAACCGCGACUG GGAUCGUCAUCCUGGCUAGUUCGCGUGAUCAGGAGAUCCGA GUAGAGGCAUAGCGAACUACGCACGGAGAAGCCUUGAGGGA AAUGCCGUAGGACCCGGGUUCGAUUCCCGGCAGCUCCACCA Mycobacterium paratuberculosis ssrA, internal partial SEQ ID NO: 71 TTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAACT GACCACCGTAAGCGTCGTTGCAAATAGATAAGCGCCGATTCA CATCAGCGCGACTTACCTCTCGCTGCCTAAGCGACAGCTAGTC CGTCAGCCCGGGAACGCCCTCGACCCGGAGCCTGGCGTCAGC TAGAGGGATCCACCGATGAGTTCGGTCGCGGGACTCATCGGG ACACCAACAGCGACTGGGATCGTCATCCTGGCTTGTTCGCGTG ACCAGGAGATCCGAGTAGAGGCATAGCGAACTGCGCACGGAG AAGCCTTGAGGGAATGCCGTAGAACCCGGGTTCGATTCCCAA Mycobacterium paratuberculosis tmRNA, internal partial SEQ ID NO: 72 UUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAC UGACCACCGUAAGCGUCGUUGCAAAUAGAUAAGCGCCGAUU CACAUCAGCGCGACUUACCUCUCGCUGCCUAAGCGACAGCU AGUCCGUCAGCCCGGGAACGCCCUCGACCCGGAGCCUGGCG UCAGCUAGAGGGAUCCACCGAUGAGUUCGGUCGCGGGACUC AUCGGGACACCAACAGCGACUGGGAUCGUCAUCCUGGCUUG UUCGCGUGACCAGGAGAUCCGAGUAGAGGCAUAGCGAACUG CGCACGGAGAAGCCUUGAGGGAAUGCCGUAGAACCCGGGUU CGAUUCCCAA Mycobacterium tuberculosis ssrA SEQ ID NO: 73 GGGGCTGAACGGTTTCGACTTCGCGCATCGAATCAAGGGAAG CGTGCCGGTGCAGGCAAGAGACCACCGTAAGCGTCGTTGCGA CCAAATAAGCGCCGATTCACATCAGCGCGACTACGCTCTCGCT GCCTAAGCGACGGCTAGTCTGTCAGACCGGGAACGCCCTCGG CCCGGACCCTGGCATCAGCTAGAGGGATCCACCGATGAGTCC GGTCGCGGGACTCCTCGGGACAACCACAGCGACTGGGATCGT CATCTCGGCTAGTTCGCGTGACCGGGAGATCCGAGCAGAGGC ATAGCGAACTGCGCACGGAGAAGCCTTGAGGGAATGCCGTAG GACCCGGGTTCGATTCCCGGCAGCTCCACCA Mycobacterium tuberculosis tmRNA SEQ ID NO: 74 GGGGCUGAACGGUUUCGACUUCGCGCAUCGAAUCAAGGGAA GCGUGCCGGUGCAGGCAAGAGACCACCGUAAGCGUCGUUGC GACCAAAUAAGCGCCGAUUCACAUCAGCGCGACUACGCUCU CGCUGCCUAAGCGACGGCUAGUCUGUCAGACCGGGAACGCC CUCGGCCCGGACCCUGGCAUCAGCUAGAGGGAUCCACCGAU GAGUCCGGUCGCGGGACUCCUCGGGACAACCACAGCGACUG GGAUCGUCAUCUCGGCUAGUUCGCGUGACCGGGAGAUCCGA GCAGAGGCAUAGCGAACUGCGCACGGAGAAGCCUUGAGGGA AUGCCGUAGGACCCGGGUUCGAUUCCCGGCAGCUCCACCA Mycoplasma capricolum ssrA SEQ ID NO: 75 GGGGATGTCATGGATTTGACAGGATATCTTTAGTACATATAAG CAGTAGTGTTGTAGACTATAAATACTACTAGGTTTAAAAAAAC GCAAATAAAAACGAAGAAACTTTTGAAATGCCAGCATTTATG ATGAATAATGCATCAGCTGGAGCAAACTTTATGTTTGCTTAAT AACTACTAGTTTAGTTATAGTATTTCACGAATTATAGATATTTT AAGCTTTATTTATAACCGTATTACCCAAGCTTAATAGAATATA TGATTGCAATAAATATATTTGAAATCTAATTGCAAATGATATT TAACCTTTAGTTAATTTTAGTTAAATATTTTAATTAGAAAATTA ACTAAACTGTAGAAAGTATGTATTAATATATCTTGGACGCGAG TTCGATTCTCGCCATCTCCACCA Mycoplasma capricolum tmRNA SEQ ID NO: 76 GGGGAUGUCAUGGAUUUGACAGGAUAUCUUUAGUACAUAU AAGCAGUAGUGUUGUAGACUAUAAAUACUACUAGGUUUAA AAAAACGCAAAUAAAAACGAAGAAACUUUUGAAAUGCCAGC AUUUAUGAUGAAUAAUGCAUCAGCUGGAGCAAACUUUAUGU UUGCUUAAUAACUACUAGUUUAGUUAUAGUAUUUCACGAAU UAUAGAUAUUUUAAGCUUUAUUUAUAACCGUAUUACCCAAG CUUAAUAGAAUAUAUGAUUGCAAUAAAUAUAUUUGAAAUC UAAUUGCAAAUGAUAUUUAACCUUUAGUUAAUUUUAGUUA AAUAUUUUAAUUAGAAAAUUAACUAAACUGUAGAAAGUAU GUAUUAAUAUAUCUUGGACGCGAGUUCGAUUCUCGCCAUCU CCACCA Mycoplasma genitalium (ATTC 33530, #1) ssrA SEQ ID NO: 77 GGGGATGTTTTGGGTTTGACATAATGCTGATAGACAAACAGT AGCATTGGGGTATGCCCCTTACAGCGCTAGGTTCAATAACCGA CAAAGAAAATAACGAAGTGTTGGTAGAACCAAATTTGATCAT TAACCAACAAGCAAGTGTTAACTTTGCTTTTGCATAAGTAGAT ACTAAAGCTACAGCTGGTGAATAGTCATAGTTTGCTAGCTGTC ATAGTTTATGACTCGAGGTTAAATCGTTCAATTTAACCTTTAA AAATAGAACTTGTTGTTTCCATGATTGTTTTGTGATCAATTGG AAACAAGACAAAAATCCACAAAACTAAAATGTAGAAGCTGTT TGTTGTGTCCTTTATGGAAACGGGTTCGATTCCCGTCATCTCC ACCA Mycoplasma genitalium (ATTC 33530, #1) tmRNA SEQ ID NO: 78 GGGGAUGUUUUGGGUUUGACAUAAUGCUGAUAGACAAACA GUAGCAUUGGGGUAUGCCCCUUACAGCGCUAGGUUCAAUAA CCGACAAAGAAAAUAACGAAGUGUUGGUAGAACCAAAUUUG AUCAUUAACCAACAAGCAAGUGUUAACUUUGCUUUUGCAUA AGUAGAUACUAAAGCUACAGCUGGUGAAUAGUCAUAGUUUG CUAGCUGUCAUAGUUUAUGACUCGAGGUUAAAUCGUUCAAU UUAACCUUUAAAAAUAGAACUUGUUGUUUCCAUGAUUGUUU UGUGAUCAAUUGGAAACAAGACAAAAAUCCACAAAACUAAA AUGUAGAAGCUGUUUGUUGUGUCCUUUAUGGAAACGGGUUC GAUUCCCGUCAUCUCCACCA Mycoplasma genitalium (ATTC 33530, #2) tmRNA, internal partial SEQ ID NO: 79 ACATAATGCTGATAGACAAACAGTAGCATTGGGGTATGCCCC TTACAGCGCTAGGTTCAATAACCGACAAAGAAAATAACGAAG TGTTGGTAGATCCAAATTTGATCATTAACCAACAAGCAAGTGT TAACTTTGCTTTTGCATAAGTAGATACTAAAGCTACAGCTGGT GAATAGTCATAGTTTGCTAGCTGTCATAGTTTATGACTCGAGG TTAAATCGTTCAATTTAACCTTTAAAAATAGAACTTGTTGTTTC CATGATTGTTTTGTGATCAATTGGAAACAAGACAAAAATCCAC AAAACTAAAATGTAGAAGCTGTTTGTTGTGTCCTTTATGGAAA CGGGTTC Mycoplasma genitalium (ATTC 33530, #2) tmRNA, internal partial SEQ ID NO: 80 ACAUAAUGCUGAUAGACAAACAGUAGCAUUGGGGUAUGCCC CUUACAGCGCUAGGUUCAAUAACCGACAAAGAAAAUAACGA AGUGUUGGUAGAUCCAAAUUUGAUCAUUAACCAACAAGCAA GUGUUAACUUUGCUUUUGCAUAAGUAGAUACUAAAGCUACA GCUGGUGAAUAGUCAUAGUUUGCUAGCUGUCAUAGUUUAUG ACUCGAGGUUAAAUCGUUCAAUUUAACCUUUAAAAAUAGAA CUUGUUGUUUCCAUGAUUGUUUUGUGAUCAAUUGGAAACAA GACAAAAAUCCACAAAACUAAAAUGUAGAAGCUGUUUGUUG UGUCCUUUAUGGAAACGGGUUC Mycoplasma pneumophila ssrA SEQ ID NO: 81 GGGGATGTAGAGGTTTTGACATAATGTTGAAAGGAAAACAGT TGCAGTGGGGTATGCCCCTTACAGCTCTAGGTATAATAACCGA CAAAAATAACGACGAAGTTTTGGTAGATCCAATGTTGATCGCT AACCAACAAGCAAGTATCAACTACGCTTTCGCTTAGAACATA CTAAAGCTACACGAATTGAATCGCCATAGTTTGGTTCGTGTCA CAGTTTATGGCTCGGGGTTAACTGGTTCAACTTAATCCTTAAA TTATGAACTTATCGTTTACTTGTTTGTCTTATGATCTAAAGTAA GCGAGACATTAAAACATAAGACTAAACTGTAGAAGCTGTTTT ACCAATCCTTTATGGAAACGGGTTCGATTCCCGTCATCTCCAC CA Mycoplasma pneumophila tmRNA SEQ ID NO: 82 GGGGAUGUAGAGGUUUUGACAUAAUGUUGAAAGGAAAACA GUUGCAGUGGGGUAUGCCCCUUACAGCUCUAGGUAUAAUAA CCGACAAAAAUAACGACGAAGUUUUGGUAGAUCCAAUGUUG AUCGCUAACCAACAAGCAAGUAUCAACUACGCUUUCGCUUA GAACAUACUAAAGCUACACGAAUUGAAUCGCCAUAGUUUGG UUCGUGUCACAGUUUAUGGCUCGGGGUUAACUGGUUCAACU UAAUCCUUAAAUUAUGAACUUAUCGUUUACUUGUUUGUCUU AUGAUCUAAAGUAAGCGAGACAUUAAAACAUAAGACUAAAC UGUAGAAGCUGUUUUACCAAUCCUUUAUGGAAACGGGUUCG AUUCCCGUCAUCUCCACCA Neisseria gonorrhoeae (ATCC 19424) ssrA, internal partial SEQ ID NO: 83 GGGGGTTGCGAAGCAGATGCGGGCATACCGGGGTCTCAGATT CCCGTAAAACACTGAATTCAAATAGTCGCAAACGACGAAACT TACGCTTTAGCCGCTTAAGGCTAGCCGTTGCAGCAGTCGGTCA ATGGGCTGTGTGGCGAAAGCCACCGCAACGTCATCTTACATTG ACTGGTTTCCAGCCGGGTTACTTGGCAGGAAATAAGACTTAA GGTAACTGGTTTCCAAAAGGCCTGTTGGTCGGCATGATGGAA ATAAGATTTTCAAATAGACACAACTAAGTATGTAGAACGCTTT GTAGAGGACTTTCGGACGGGG Neisseria gonorrhoeae (ATCC 19424) tmRNA, internal partial SEQ ID NO: 84 GGGGGUUGCGAAGCAGAUGCGGGCAUACCGGGGUCUCAGAU UCCCGUAAAACACUGAAUUCAAAUAGUCGCAAACGACGAAA CUUACGCUUUAGCCGCUUAAGGCUAGCCGUUGCAGCAGUCG GUCAAUGGGCUGUGUGGCGAAAGCCACCGCAACGUCAUCUU ACAUUGACUGGUUUCCAGCCGGGUUACUUGGCAGGAAAUAA GACUUAAGGUAACUGGUUUCCAAAAGGCCUGUUGGUCGGCA UGAUGGAAAUAAGAUUUUCAAAUAGACACAACUAAGUAUG UAGAACGCUUUGUAGAGGACUUUCGGACGGGG Neisseria gonorrhoeae (FA 1090) ssrA SEQ ID NO: 85 GGGGGCGACCTTGGTTTCGACGGGGGTTGCGAAGCAGATGCG GGCATACCGGGGTCTCAGATTCCCGTAAAACACTGAATTCAA ATAGTCGCAAACGACGAAACTTACGCTTTAGCCGCTTAAGGCT AGCCGTTGCAGCAGTCGGTCAATGGGCTGTGTGGTGAAAGCC ACCGCAACGTCATCTTACATTGACTGGTTTCCAGCCGGGTTAC TTGGCAGGAAATAAGACTTAAGGTAACTGGTTTCCAAAAGGC CTGTTGGTCGGCATGATGGAAATAAGATTTTCAAATAGACAC AACTAAGTATGTAGAACGCTTTGTAGAGGACTTTCGGACGGG GGTTCGATTCCCCCCGCCTCCACCA Neisseria gonorrhoeae (FA 1090) tmRNA SEQ ID NO: 86 GGGGGCGACCUUGGUUUCGACGGGGGUUGCGAAGCAGAUGC GGGCAUACCGGGGUCUCAGAUUCCCGUAAAACACUGAAUUC AAAUAGUCGCAAACGACGAAACUUACGCUUUAGCCGCUUAA GGCUAGCCGUUGCAGCAGUCGGUCAAUGGGCUGUGUGGUGA AAGCCACCGCAACGUCAUCUUACAUUGACUGGUUUCCAGCC GGGUUACUUGGCAGGAAAUAAGACUUAAGGUAACUGGUUUC CAAAAGGCCUGUUGGUCGGCAUGAUGGAAAUAAGAUUUUCA AAUAGACACAACUAAGUAUGUAGAACGCUUUGUAGAGGACU UUCGGACGGGGGUUCGAUUCCCCCCGCCUCCACCA Neisseria meningitidis ssrA SEQ ID NO: 87 GGGGGCGACCTTGGTTTCGACGGGGGTTGCGAAGCAGATGCG GGCATACCGGGGTCTCAGATTCCCGTAAAACACTGAATTCAA ATAGTCGCAAACGACGAAACTTACGCTTTAGCCGCTTAAGGCT AGCCGTTGCAGCAGTCGGTCAATGGGCTGTGTGGCGAAAGCC ACCGCAACGTCATCTTACATTGACTGGTTTCCTGCCGGGTTAT TTGGCAGGAAATGAGATTTAAGGTAACTGGTTTCCAAAAGGC CTGTTGGTCGGCATGATGGAAATAAGATTTTCAAATAGACAC AACTAAGTATGTAGAACGCTTTGTAGAGGACTTTCGGACGGG GGTTCGATTCCCCCCGCCTCCACCA Neisseria meningitidis tmRNA SEQ ID NO: 88 GGGGGCGACCUUGGUUUCGACGGGGGUUGCGAAGCAGAUGC GGGCAUACCGGGGUCUCAGAUUCCCGUAAAACACUGAAUUC AAAUAGUCGCAAACGACGAAACUUACGCUUUAGCCGCUUAA GGCUAGCCGUUGCAGCAGUCGGUCAAUGGGCUGUGUGGCGA AAGCCACCGCAACGUCAUCUUACAUUGACUGGUUUCCUGCC GGGUUAUUUGGCAGGAAAUGAGAUUUAAGGUAACUGGUUU CCAAAAGGCCUGUUGGUCGGCAUGAUGGAAAUAAGAUUUUC AAAUAGACACAACUAAGUAUGUAGAACGCUUUGUAGAGGAC UUUCGGACGGGGGUUCGAUUCCCCCCGCCUCCACCA Nostoc muscorum PCC7120 ssrA SEQ ID NO: 89 GGGTCCGTCGGTTTCGACAGGTTGGCGAACGCTACTCTGTGAT TCAGGTCGAGAGTGAGTCTCCTCTGCAAATCAAGGCTCAAAA CAAAAGTAAATGCGAATAACATCGTTAAATTTGCTCGTAAGG ACGCTCTAGTAGCTGCCTAAATAGCCTCTTTCAGGTTCGAGCG TCTTCGGTTTGACTCCGTTAAGGACTGAAGACCAACCCCCAAC GGATGCTCTAGCAATGTTCTCTGGTTGGCTTGCTAGCTAAGAT TTAATCAGAGCATCCTACGTTCGGGATAATGAACGATTCCCGC CTTGAGGGTCAGAAAGGCTAAACCTGTGAATGAGCGGGGGGT CAATACCCAATTTGGACAGCAGTTCGACTCTGCTCGATCCACCA Nostoc muscorum PCC7120 tmRNA SEQ ID NO: 90 GGGUCCGUCGGUUUCGACAGGUUGGCGAACGCUACUCUGUG AUUCAGGUCGAGAGUGAGUCUCCUCUGCAAAUCAAGGCUCA AAACAAAAGUAAAUGCGAAUAACAUCGUUAAAUUUGCUCGU AAGGACGCUCUAGUAGCUGCCUAAAUAGCCUCUUUCAGGUU CGAGCGUCUUCGGUUUGACUCCGUUAAGGACUGAAGACCAA CCCCCAACGGAUGCUCUAGCAAUGUUCUCUGGUUGGCUUGC UAGCUAAGAUUUAAUCAGAGCAUCCUACGUUCGGGAUAAUG AACGAUUCCCGCCUUGAGGGUCAGAAAGGCUAAACCUGUGA AUGAGCGGGGGGUCAAUACCCAAUUUGGACAGCAGUUCGAC UCUGCUCGAUCCACCA Odontella sinensis (diatom) chloroplast ssrA SEQ ID NO: 91 GGGGCTGACTTGGTTTCGACATTTAAAAATTGTTACAGTATGA TGCAGGTCGAAGTTTCTAATCTTCGTAAAAAAAGAGAAATTTA TAATAAATGCTAATAATTTAATTTCTTCTGTGTTTAAAAGTTTA TCAACTAAGCAAAATAGTTTAAATTTAAGTTTTGCTGTTTAAG TTTTATGCACATTTAATGATCTAGTAAATAACTTTGTTCGCTAT AATTTATATTTATAACTAGACTTTTGTCTTTTTTATAGTTTAGA ATAACTTTATCATTTCAAACCTCGTTCCATCTAGTTGAACTAA ACCTGTGAACGAATACTATAATAAAATTTTTAGATGGACGTGG GTTCGACTCCCATCAGCTCCACCA Odontella sinensis (diatom) chloroplast tmRNA SEQ ID NO: 92 GGGGCUGACUUGGUUUCGACAUUUAAAAAUUGUUACAGUAU GAUGCAGGUCGAAGUUUCUAAUCUUCGUAAAAAAAGAGAAA UUUAUAAUAAAUGCUAAUAAUUUAAUUUCUUCUGUGUUUA AAAGUUUAUCAACUAAGCAAAAUAGUUUAAAUUUAAGUUU UGCUGUUUAAGUUUUAUGCACAUUUAAUGAUCUAGUAAAU AACUUUGUUCGCUAUAAUUUAUAUUUAUAACUAGACUUUUG UCUUUUUUAUAGUUUAGAAUAACUUUAUCAUUUCAAACCUC GUUCCAUCUAGUUGAACUAAACCUGUGAACGAAUACUAUAA UAAAAUUUUUAGAUGGACGUGGGUUCGACUCCCAUCAGCUC CACCA Porphyra purpureum (red alga) chloroplast ssrA SEQ ID NO: 93 GGGGCTGCAAGGTTTCTACATTGTGAAAAAACAAATATATGA AAGTAAAACGAGCTCATTATTAGAGCTTTTAGTTAAATAAATG CAGAAAATAATATTATTGCTTTTTCTCGAAAATTAGCTGTTGC ATAAATAGTCTCAATTTTTGTAATTCGAAGTGATAGACTCTTA TACACTACGAATATTCTGTTAGAGTTGCTCTTAATAAAAGAAA AGTAAAAAAATACAAATTCTTATGTTTTTTACCTGAATTGATT CAATTTAAGGTTAGTATTTTTTGATTTTTACAATGGACGTGGG TTCAAGTCCCACCAGCTCCACCA Porphyra purpureum (red alga) chloroplast tmRNA SEQ ID NO: 94 GGGGCUGCAAGGUUUCUACAUUGUGAAAAAACAAAUAUAUG AAAGUAAAACGAGCUCAUUAUUAGAGCUUUUAGUUAAAUA AAUGCAGAAAAUAAUAUUAUUGCUUUUUCUCGAAAAUUAGC UGUUGCAUAAAUAGUCUCAAUUUUUGUAAUUCGAAGUGAU AGACUCUUAUACACUACGAAUAUUCUGUUAGAGUUGCUCUU AAUAAAAGAAAAGUAAAAAAAUACAAAUUCUUAUGUUUUU UACCUGAAUUGAUUCAAUUUAAGGUUAGUAUUUUUUGAUU UUUACAAUGGACGUGGGUUCAAGUCCCACCAGCUCCACCA Porphyromonas gingivalis ssrA SEQ ID NO: 95 GGGGCTGACCGGCTTTGACAGCGTGATGAAGCGGTATGTAAG CATGTAGTGCGTGGGTGGCTTGCACTATAATCTCAGACATCAA AAGTTTAATTGGCGAAAATAACTACGCTCTCGCTGCGTAATCG AAGAATAGTAGATTAGACGCTTCATCGCCGCCAAAGTGGCAG CGACGAGACATCGCCCGAGCAGCTTTTTCCCGAAGTAGCTCG ATGGTGCGGTGCTGACAAATCGGGAACCGCTACAGGATGCTT CCTGCCTGTGGTCAGATCGAACGGAAGATAAGGATCGTGCAT TGGGTCGTTTCAGCCTCCGCTCGCTCACGAAAATTCCAACTGA AACTAAACATGTAGAAAGCATATTGATTCCATGTTTGGACGA GGGTTCAATTCCCTCCAGCTCCACCA Porphyromonas gingivalis tmRNA SEQ ID NO: 96 GGGGCUGACCGGCUUUGACAGCGUGAUGAAGCGGUAUGUAA GCAUGUAGUGCGUGGGUGGCUUGCACUAUAAUCUCAGACAU CAAAAGUUUAAUUGGCGAAAAUAACUACGCUCUCGCUGCGU AAUCGAAGAAUAGUAGAUUAGACGCUUCAUCGCCGCCAAAG UGGCAGCGACGAGACAUCGCCCGAGCAGCUUUUUCCCGAAG UAGCUCGAUGGUGCGGUGCUGACAAAUCGGGAACCGCUACA GGAUGCUUCCUGCCUGUGGUCAGAUCGAACGGAAGAUAAGG AUCGUGCAUUGGGUCGUUUCAGCCUCCGCUCGCUCACGAAA AUUCCAACUGAAACUAAACAUGUAGAAAGCAUAUUGAUUCC AUGUUUGGACGAGGGUUCAAUUCCCUCCAGCUCCACCA Proteus rettgeri ssrA (NCTC 10975), internal partial SEQ ID NO: 97 GGGATTTGCGAAACCCAAGGTGCATGCCGAGGGGCGGTTGGC CTCGTAAAAAGCCGCAAAAAAATAGTCGCAAACGACGAAAAC TACGCTTTAGCAGCTTAATAACCTGCTTAGAGCCCTCTCTCCC TAGCCTCCGCTCTTGGACGGGGATCAAGAGAGGTCAAACCCA AAAGAGATCGCGTGGATGCCTTGCCTGGGGTTGAAGCGTTAA ACTTAATCAGGATAGTTTGTTGGTGGCGTGTCTGTCCGCAGCT GGCAAATGAATTCAAAGACTAGACTAAGCATGTAGTACCGAG GATGTAGAAATTTC Proteus rettgeri tmRNA (NCTC 10975), internal partial SEQ ID NO: 98 GGGAUUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUUGG CCUCGUAAAAAGCCGCAAAAAAAUAGUCGCAAACGACGAAA ACUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUC UCCCUAGCCUCCGCUCUUGGACGGGGAUCAAGAGAGGUCAA ACCCAAAAGAGAUCGCGUGGAUGCCUUGCCUGGGGUUGAAG CGUUAAACUUAAUCAGGAUAGUUUGUUGGUGGCGUGUCUGU CCGCAGCUGGCAAAUGAAUUCAAAGACUAGACUAAGCAUGU AGUACCGAGGAUGUAGAAAUUUC Pseudoalteromonas haloplanktoni ssrA, internal partial SEQ ID NO: 99 GGAATTCAAGAAGCCCGAGGTGCATGTCGAGGTGCGGTTTGC CTCGTAAAAAAGCCGCAATTTAAAGTAATCGCAAACGACGAT AACTACTCTCTAGCAGCTTAGGCTGGCTAGCGCTCCTTCCATG TATTCTTGTGGACTGGATTTTGGAGTGTCACCCTAACACCTGA TCGCGACGGAAACCCTGGCCGGGGTTGAAGCGTTAAAACTAA GCGGCCTCGCCTTTATCTACCGTGTTTGTCCGGGATTTAAAGG TTAATTAAATGACAATACTAAACATGTAGTACCGACGGTCGA GGCTTTTCGGACGGGG Pseudoalteromonas haloplanktoni tmRNA, internal partial SEQ ID NO: 100 GGAAUUCAAGAAGCCCGAGGUGCAUGUCGAGGUGCGGUUUG CCUCGUAAAAAAGCCGCAAUUUAAAGUAAUCGCAAACGACG AUAACUACUCUCUAGCAGCUUAGGCUGGCUAGCGCUCCUUC CAUGUAUUCUUGUGGACUGGAUUUUGGAGUGUCACCCUAAC ACCUGAUCGCGACGGAAACCCUGGCCGGGGUUGAAGCGUUA AAACUAAGCGGCCUCGCCUUUAUCUACCGUGUUUGUCCGGG AUUUAAAGGUUAAUUAAAUGACAAUACUAAACAUGUAGUA CCGACGGUCGAGGCUUUUCGGACGGGG Pseudomonas aeruginosa ssrA SEQ ID NO: 101 GGGGCCGATTAGGATTCGACGCCGGTAACAAAAGTTGAGGGG CATGCCGAGTTGGTAGCAGAACTCGTAAATTCGCTGCTGCAA ACTTATAGTTGCCAACGACGACAACTACGCTCTAGCTGCTTAA TGCGGCTAGCAGTCGCTAGGGGATGCCTGTAAACCCGAAACG ACTGTCAGATAGAACAGGATCGCCGCCAAGTTCGCTGTAGAC GTAACGGCTAAAACTCATACAGCTCGCTCCAAGCACCCTGCC ACTCGGGCGGCGCGGAGTTAACTCAGTAGAGCTGGCTAAGCA TGTAAAACCGATAGCGGAAAGCTGGCGGACGGGGGTTCAAAT CCCCCCGGTTCCACCA Pseudomonas aeruginosa tmRNA SEQ ID NO: 102 GGGGCCGAUUAGGAUUCGACGCCGGUAACAAAAGUUGAGGG GCAUGCCGAGUUGGUAGCAGAACUCGUAAAUUCGCUGCUGC AAACUUAUAGUUGCCAACGACGACAACUACGCUCUAGCUGC UUAAUGCGGCUAGCAGUCGCUAGGGGAUGCCUGUAAACCCG AAACGACUGUCAGAUAGAACAGGAUCGCCGCCAAGUUCGCU GUAGACGUAACGGCUAAAACUCAUACAGCUCGCUCCAAGCA CCCUGCCACUCGGGCGGCGCGGAGUUAACUCAGUAGAGCUG GCUAAGCAUGUAAAACCGAUAGCGGAAAGCUGGCGGACGGG GGUUCAAAUCCCCCCGGUUCCACCA Salmonella typhimurium ssrA SEQ ID NO: 103 GGGGCTGATTCTGGATTCGACGGGATTTGCGAAACCCAAGGT GCATGCCGAGGGGCGGTTGGCCTCGTAAAAAGCCGCAAAAAA ATAGTCGCAAACGACGAAACCTACGCTTTAGCAGCTTAATAA CCTGCTTAGAGCCCTCTCTCCCTAGCCTCCGCTCTTAGGACGG GGATCAAGAGAGGTCAAACCCAAAAGAGATCGCGCGGATGCC CTGCCTGGGGTTGAAGCGTTAAAACGAATCAGGCTAGTCTGG TAGTGGCGTGTCCGTCCGCAGGTGCCAGGCGAATGTAAAGAC TGACTAAGCATGTAGTACCGAGGATGTAGGAATTTCGGACGC GGGTTCAACTCCCGCCAGCTCCACCA Salmonella typhimurium tmRNA SEQ ID NO: 104 GGGGCUGAUUCUGGAUUCGACGGGAUUUGCGAAACCCAAGG UGCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAA AAAUAGUCGCAAACGACGAAACCUACGCUUUAGCAGCUUAA UAACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAG GACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCGCGCG GAUGCCCUGCCUGGGGUUGAAGCGUUAAAACGAAUCAGGCU AGUCUGGUAGUGGCGUGUCCGUCCGCAGGUGCCAGGCGAAU GUAAAGACUGACUAAGCAUGUAGUACCGAGGAUGUAGGAAU UUCGGACGCGGGUUCAACUCCCGCCAGCUCCACCA Shewanella putrefaciens ssrA SEQ ID NO: 105 GGGGGCGATTCTGGATTCGACAGGATTCACGAAACCCTGGGA GCATGCCGAGGGGCGGTTGGCCTCGTAAAAAGCCGCAAAGTT ATAGTTGCAAACGACGATAACTACGCTCTAGCCGCTTAATGCC GCTAGCCATCTACCACACGCTTTGCACATGGGCAGTGGATTTG ATGGTCATCTCACATCGTGCTAGCGAGGGAACCCTGTCTGGGG GTGAACCGCGAAACAGTACCGGACTCACCGTGTGGGATCCTG TCTTTCGGAGTTCAAACGGTTAAACAATAGAAAGACTAAGCA TGTAGCGCCTTGGATGTAGGTTTTCTGGACGCGGGTTCAAGTC CCGCCGCCTCCACCA Shewanella putrefaciens tmRNA SEQ ID NO: 106 GGGGGCGAUUCUGGAUUCGACAGGAUUCACGAAACCCUGGG AGCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAG UUAUAGUUGCAAACGACGAUAACUACGCUCUAGCCGCUUAA UGCCGCUAGCCAUCUACCACACGCUUUGCACAUGGGCAGUG GAUUUGAUGGUCAUCUCACAUCGUGCUAGCGAGGGAACCCU GUCUGGGGGUGAACCGCGAAACAGUACCGGACUCACCGUGU GGGAUCCUGUCUUUCGGAGUUCAAACGGUUAAACAAUAGAA AGACUAAGCAUGUAGCGCCUUGGAUGUAGGUUUUCUGGACG CGGGUUCAAGUCCCGCCGCCUCCACCA Staphylococcus aureus ssrA SEQ ID NO: 107 GGGGACGTTCATGGATTCGACAGGGGTCCCCCGAGCTCATTA AGCGTGTCGGAGGGTTGTCTTCGTCATCAACACACACAGTTTA TAATAACTGGCAAATCAAACAATAATTTCGCAGTAGCTGCCTA ATCGCACTCTGCATCGCCTAACAGCATTTCCTATGTGCTGTTA ACGCGATTCAACCTTAATAGGATATGCTAAACACTGCCGTTTG AAGTCTGTTTAGAAGAAACTTAATCAAACTAGCATCATGTTGG TTGTTTATCACTTTTCATGATGCGAAACCTATCGATAAACTAC ACACGTAGAAAGATGTGTATCAGGACCTTTGGACGCGGGTTC AAATCCCGCCGTCTCCACCA Staphylococcus aureus tmRNA SEQ ID NO: 108 GGGGACGUUCAUGGAUUCGACAGGGGUCCCCCGAGCUCAUU AAGCGUGUCGGAGGGUUGUCUUCGUCAUCAACACACACAGU UUAUAAUAACUGGCAAAUCAAACAAUAAUUUCGCAGUAGCU GCCUAAUCGCACUCUGCAUCGCCUAACAGCAUUUCCUAUGU GCUGUUAACGCGAUUCAACCUUAAUAGGAUAUGCUAAACAC UGCCGUUUGAAGUCUGUUUAGAAGAAACUUAAUCAAACUAG CAUCAUGUUGGUUGUUUAUCACUUUUCAUGAUGCGAAACCU AUCGAUAAACUACACACGUAGAAAGAUGUGUAUCAGGACCU UUGGACGCGGGUUCAAAUCCCGCCGUCUCCACCA Streptococcus gordonii ssrA SEQ ID NO: 109 GGGGTCGTTACGGATTCGACAGGCATTATGAGGCATATTTTGC GACTCATCTAGCGGATGTAAAACGCCAGTTAAATATAACTGC AAAAAATAATACTTCTTACGCTTTAGCTGCCTAAAAACCAGCG GGCGTGACCCGATTCGGATTGCTTGTGTCTGATGACAGGTCTT ATTATTAGCAAGCTACGGTAGAATCTTGTCTAGTGATTTTACA AGAGATTGATAGACTCGCTTGATTTGGGCTTGAGTTATGTGTC AAAATCAAGTTAAAACAATACATAGCCTATGGTTGTAGACAA ATGTGTTGGCAGATGTTTGGACGTGGGTTCGACTCCCACCGGC TCCACCA Streptococcus gordonii tmRNA SEQ ID NO: 110 GGGGUCGUUACGGAUUCGACAGGCAUUAUGAGGCAUAUUUU GCGACUCAUCUAGCGGAUGUAAAACGCCAGUUAAAUAUAAC UGCAAAAAAUAAUACUUCUUACGCUUUAGCUGCCUAAAAAC CAGCGGGCGUGACCCGAUUCGGAUUGCUUGUGUCUGAUGAC AGGUCUUAUUAUUAGCAAGCUACGGUAGAAUCUUGUCUAGU GAUUUUACAAGAGAUUGAUAGACUCGCUUGAUUUGGGCUUG AGUUAUGUGUCAAAAUCAAGUUAAAACAAUACAUAGCCUAU GGUUGUAGACAAAUGUGUUGGCAGAUGUUUGGACGUGGGU UCGACUCCCACCGGCUCCACCA Streptococcus mutans ssrA SEQ ID NO: 111 GGGGTCGTTACGGATTCGACAGGCATTATGAGACCTATTTTGC GACTCATCTAGCGGATGTAAAACGCCAGTTAAATATAACTGC AAAAAATACAAATTCTTACGCAGTAGCTGCCTAAAAACCAGC CTGTGTGATCAATAACAAATTGCTTGTGTTTGTTGATTGGTCTT ATTGTTAACAAGCTACGTTAGAACTGAGTCAGGCTGTTCTAAA AGAGTTCTACTGACTCGCATCGTTAGAGTTTGAGTTATGTATT GTAACGGTGTTAAATAAACACATAACCTATAGTTGTAGACAA ATGGGTTAGCAGATGTTTGGACGTGGGTTCGACTCCCACCGGC TCCACCA Streptococcus mutans tmRNA SEQ ID NO: 112 GGGGUCGUUACGGAUUCGACAGGCAUUAUGAGACCUAUUUU GCGACUCAUCUAGCGGAUGUAAAACGCCAGUUAAAUAUAAC UGCAAAAAAUACAAAUUCUUACGCAGUAGCUGCCUAAAAAC CAGCCUGUGUGAUCAAUAACAAAUUGCUUGUGUUUGUUGAU UGGUCUUAUUGUUAACAAGCUACGUUAGAACUGAGUCAGGC UGUUCUAAAAGAGUUCUACUGACUCGCAUCGUUAGAGUUUG AGUUAUGUAUUGUAACGGUGUUAAAUAAACACAUAACCUAU AGUUGUAGACAAAUGGGUUAGCAGAUGUUUGGACGUGGGU UCGACUCCCACCGGCUCCACCA Streptococcus pneumoniae ssrA SEQ ID NO: 113 GGGGTCGTTACGGATTCGACAGGCATTATGAGGCATATTTTGC GACTCGTGTGGCGACGTAAACGCTCAGTTAAATATAACTGCA AAAAATAACACTTCTTACGCTCTAGCTGCCTAAAAACCAGCA GGCGTGACCCGATTTGGATTGCTCGTGTTCAATGACAGGTCTT ATTATTAGCGAGATACGATTAAGCCTTGTCTAGCGGTTTGATA AGAGATTGATAGACTCGCAGTTTCTAGACTTGAGTTATGTGTC GAGGGGCTGTTAAAATAATACATAACCTATGGTTGTAGACAA ATATGTTGGCAGGTGTTTGGACGTGGGTTCGACTCCCACCGGC TCCACCA Streptococcus pneumoniae tmRNA SEQ ID NO: 114 GGGGUCGUUACGGAUUCGACAGGCAUUAUGAGGCAUAUUUU GCGACUCGUGUGGCGACGUAAACGCUCAGUUAAAUAUAACU GCAAAAAAUAACACUUCUUACGCUCUAGCUGCCUAAAAACC AGCAGGCGUGACCCGAUUUGGAUUGCUCGUGUUCAAUGACA GGUCUUAUUAUUAGCGAGAUACGAUUAAGCCUUGUCUAGCG GUUUGAUAAGAGAUUGAUAGACUCGCAGUUUCUAGACUUGA GUUAUGUGUCGAGGGGCUGUUAAAAUAAUACAUAACCUAUG GUUGUAGACAAAUAUGUUGGCAGGUGUUUGGACGUGGGUU CGACUCCCACCGGCUCCACCA Streptococcus pyogenes ssrA SEQ ID NO: 115 GGGGTTGTTACGGATTCGACAGGCATTATGAGGCATGTTTTGC GTCCCATCGGCAGATGTAAATTGCCAGTTAAATATAACTGCAA AAAATACAAACTCTTACGCTTTAGCTGCCTAAAAACCAGCTAG CGTGACTTCTACAAGATTGCTTGTGTCCTGTTAGAAGTCTCAA AATAGCAAGCTACGGTTACGAAATTGTCTAGTTTCGTGACAAG AGATTGATAGACTCGCAAACTAATGGCTTGAGTTATGTGTCTT TAGTTTGTTAAATGAAGACATAACCTATGGACGTAGACAAAT ATGTTGGCAGGTGTTTGGACGTGGGTTCGACTCCCACCAGCTC CACCA Streptococcus pyogenes tmRNA SEQ ID NO: 116 GGGGUUGUUACGGAUUCGACAGGCAUUAUGAGGCAUGUUUU GCGUCCCAUCGGCAGAUGUAAAUUGCCAGUUAAAUAUAACU GCAAAAAAUACAAACUCUUACGCUUUAGCUGCCUAAAAACC AGCUAGCGUGACUUCUACAAGAUUGCUUGUGUCCUGUUAGA AGUCUCAAAAUAGCAAGCUACGGUUACGAAAUUGUCUAGUU UCGUGACAAGAGAUUGAUAGACUCGCAAACUAAUGGCUUGA GUUAUGUGUCUUUAGUUUGUUAAAUGAAGACAUAACCUAU GGACGUAGACAAAUAUGUUGGCAGGUGUUUGGACGUGGGU UCGACUCCCACCAGCUCCACCA Synechococcus sp. PCC6301 ssrA SEQ ID NO: 117 GGGGCTGTAATGGTTTCGACGTGTTGGTGAATCCTTCACCGTG ATTCAGGCCGAGAGGGAGTCCACTCTCGTAAATCCAGGCTCA ACCAAAAGTAACTGCGAACAACATCGTTCCTTTCGCTCGTAAG GCTGCTCCTGTAGCTGCTTAAACGCCACAAACTTTCTGGCTCGAGCG TCTAGTCGTAGACTCCGTTAATACGCCTAGACTTAAACCCCCA ACGGATGCTCGAGTGGCGGCCTCAGGTCCGTCCTCTCGCTAAG CAAAAACCTGAGCATCCCGCCAACGGGGATAATCGTTGGCTC CCGCACAGTGGGTCAACCGTGCTAAGCCTGTGAACGAGCGGA AAGTTACTAGTCAATGCGGACAGCGGTTCGATTCCGCTCAGCT CCACCA Synechococcus sp. PCC6301 tmRNA SEQ ID NO: 118 GGGGCUGUAAUGGUUUCGACGUGUUGGUGAAUCCUUCACCG UGAUUCAGGCCGAGAGGGAGUCCACUCUCGUAAAUCCAGGC UCAACCAAAAGUAACUGCGAACAACAUCGUUCCUUUCGCUC GUAAGGCUGCUCCUGUAGCUGCUUAAACGCCACAAACUUUC UGGCUCGAGCGUCUAGUCGUAGACUCCGUUAAUACGCCUAG ACUUAAACCCCCAACGGAUGCUCGAGUGGCGGCCUCAGGUC CGUCCUCUCGCUAAGCAAAAACCUGAGCAUCCCGCCAACGG GGAUAAUCGUUGGCUCCCGCACAGUGGGUCAACCGUGCUAA GCCUGUGAACGAGCGGAAAGUUACUAGUCAAUGCGGACAGC GGUUCGAUUCCGCUCAGCUCCACCA Synechocystis sp. PCC6803 ssrA SEQ ID NO: 119 GGGGCCGCAATGGTTTCGACAGGTTGGCGAAAGCTTGCCCGT GATACAGGTCGAGAGTGAGTCTCCTCTCGCAAATCAAAGGCT CAAAAAAAAGTAACTGCGAATAACATCGTCAGCTTCAAACGG GTAGCCATAGCAGCCTAGTCTGTAAAAGCTACATTTTCTTGTC AAAGACCGTTTACTTCTTTTCTGACTCCGTTAAGGATTAGAGG TTAACCCCAACGGATGCTTTGTTTGGCTCTTCTCTAGTTAGCTA AACAATCAAGACTCAGACTAGAGCATCCCACCATCAGGGATA ATCGATGGTCCCCGTCCTAGGGCTAGAAGGACTAAACCTGTG AATGAGCGGAAAGTTAATACCCAGTTTGGACAGCAGTTCAAT TCTGCTCGGCTCCACCA Synechocystis sp. PCC6803 tmRNA SEQ ID NO: 120 GGGGCCGCAAUGGUUUCGACAGGUUGGCGAAAGCUUGCCCG UGAUACAGGUCGAGAGUGAGUCUCCUCUCGCAAAUCAAAGG CUCAAAAAAAAGUAACUGCGAAUAACAUCGUCAGCUUCAAA CGGGUAGCCAUAGCAGCCUAGUCUGUAAAAGCUACAUUUUC UUGUCAAAGACCGUUUACUUCUUUUCUGACUCCGUUAAGGA UUAGAGGUUAACCCCAACGGAUGCUUUGUUUGGCUCUUCUC UAGUUAGCUAAACAAUCAAGACUCAGACUAGAGCAUCCCAC CAUCAGGGAUAAUCGAUGGUCCCCGUCCUAGGGCUAGAAGG ACUAAACCUGUGAAUGAGCGGAAAGUUAAUACCCAGUUUGG ACAGCAGUUCAAUUCUGCUCGGCUCCACCA Thermotoga maritima ssrA SEQ ID NO: 121 GGGGGCGAACGGGTTCGACGGGGATGGAGTCCCCTGGGAAGC GAGCCGAGGTCCCCACCTCCTCGTAAAAAAGGTGGGACAAAG AATAAGTGCCAACGAACCTGTTGCTGTTGCCGCTTAATAGATA AGCGGCCGTCCTCTCCGAAGTTGGCTGGGCTTCGGAAGAGGG CGTGAGAGATCCAGCCTACCGATTCAGCTTCGCCTTCCGGCCT GAATCGGGAAAACTCAGGAAGGCTGTGGGAGAGGACACCCTG CCCGTGGGAGGTCCCTCCCGAGAGCGAAAACACGGGCTGCGC TCGGAGAAGCCCAGGGGCCTCCATCTTCGGACGGGGGTTCGA ATCCCCCCGCCTCCACCA Thermotoga maritima tmRNA SEQ ID NO: 122 GGGGGCGAACGGGUUCGACGGGGAUGGAGUCCCCUGGGAAG CGAGCCGAGGUCCCCACCUCCUCGUAAAAAAGGUGGGACAA AGAAUAAGUGCCAACGAACCUGUUGCUGUUGCCGCUUAAUA GAUAAGCGGCCGUCCUCUCCGAAGUUGGCUGGGCUUCGGAA GAGGGCGUGAGAGAUCCAGCCUACCGAUUCAGCUUCGCCUU CCGGCCUGAAUCGGGAAAACUCAGGAAGGCUGUGGGAGAGG ACACCCUGCCCGUGGGAGGUCCCUCCCGAGAGCGAAAACAC GGGCUGCGCUCGGAGAAGCCCAGGGGCCUCCAUCUUCGGAC GGGGGUUCGAAUCCCCCCGCCUCCACCA Thermus thermophilus ssrA SEQ ID NO: 123 GGGGGTGAAACGGTCTCGACGGGGGTCGCCGAGGGCGTGGCT GCGCGCCGAGGTGCGGGTGGCCTCGTAAAAACCCGCAACGGC ATAACTGCCAACACCAACTACGCTCTCGCGGCTTAATGACCGC GACCTCGCCCGGTAGCCCTGCCGGGGGCTCACCGGAAGCGGG GACACAAACCCGGCTAGCCCGGGGCCACGCCCTCTAACCCCG GGCGAAGCTTGAAGGGGGCTCGCTCCTGGCCGCCCGTCCGCG GGCCAAGCCAGGAGGACACGCGAAACGCGGACTACGCGCGT AGAGGCCCGCCGTAGAGACCTTCGGACGGGGGTTCGACTCCC CCCACCTCCACCA Thermus thermophilus tmRNA SEQ ID NO: 124 GGGGGUGAAACGGUCUCGACGGGGGUCGCCGAGGGCGUGGC UGCGCGCCGAGGUGCGGGUGGCCUCGUAAAAACCCGCAACG GCAUAACUGCCAACACCAACUACGCUCUCGCGGCUUAAUGA CCGCGACCUCGCCCGGUAGCCCUGCCGGGGGCUCACCGGAAG CGGGGACACAAACCCGGCUAGCCCGGGGCCACGCCCUCUAAC CCCGGGCGAAGCUUGAAGGGGGCUCGCUCCUGGCCGCCCGU CCGCGGGCCAAGCCAGGAGGACACGCGAAACGCGGACUACG CGCGUAGAGGCCCGCCGUAGAGACCUUCGGACGGGGGUUCG ACUCCCCCCACCUCCACCA Treponema pallidum ssrA SEQ ID NO: 125 GGGGATGACTAGGTTTCGACTAGGGATGTGGGGTGTTGCGCT GCAGGTGGAGTGTCGATCTCCTGATTCGGCGCCTTTATAACTG CCAATTCTGACAGTTTCGACTACGCGCTCGCCGCGTAATCGCG GGCCTGTGTTTGCGCTGCTCTGAGCGAACATATCGGCCCGACG CCAAACGGAGCTTGCTCTTACGTTGTGCACGGCGGACGTAGG GGGACTTTTGTCTGTGCTAAGACTCTGGCGCGTGCGGTGCAGG CCTAGCAGAGTCCGACAAACGCAGTACGCACCGCTAAACCTG TAGGCGCGCAGCACTCGCTCTTTAGGACGGGGGTTCGATTCCC CCCATCTCCACCA Treponema pallidum tmRNA SEQ ID NO: 126 GGGGAUGACUAGGUUUCGACUAGGGAUGUGGGGUGUUGCGC UGCAGGUGGAGUGUCGAUCUCCUGAUUCGGCGCCUUUAUAA CUGCCAAUUCUGACAGUUUCGACUACGCGCUCGCCGCGUAA UCGCGGGCCUGUGUUUGCGCUGCUCUGAGCGAACAUAUCGG CCCGACGCCAAACGGAGCUUGCUCUUACGUUGUGCACGGCG GACGUAGGGGGACUUUUGUCUGUGCUAAGACUCUGGCGCGU GCGGUGCAGGCCUAGCAGAGUCCGACAAACGCAGUACGCAC CGCUAAACCUGUAGGCGCGCAGCACUCGCUCUUUAGGACGG GGGUUCGAUUCCCCCCAUCUCCACCA Vibrio cholerae ssrA SEQ ID NO: 127 GGGGCTGATTCAGGATTCGACGGGAATTTTGCAGTCTGAGGT GCATGCCGAGGTGCGGTAGGCCTCGTTAACAAACCGCAAAAA AATAGTCGCAAACGACGAAAACTACGCACTAGCAGCTTAATA CCCTGCTCAGAGCCCTTCCTCCCTAGCTTCCGCTTGTAAGACG GGGAAATCAGGAAGGTCAAACCAAATCAAGCTGGCGTGGATT CCCCCACCTGAGGGATGAAGCGCGAGATCTAATTCAGGTTAG CCATTCGTTAGCGTGTCGGTTCGCAGGCGGTGGTGAAATTAAA GATCGACTAAGCATGTAGTACCAAAGATGAATGGTTTTCGGA CGGGGGTTCAACTCCCCCCAGCTCCACCA Vibrio cholerae tmRNA SEQ ID NO: 128 GGGGCUGAUUCAGGAUUCGACGGGAAUUUUGCAGUCUGAGG UGCAUGCCGAGGUGCGGUAGGCCUCGUUAACAAACCGCAAA AAAAUAGUCGCAAACGACGAAAACUACGCACUAGCAGCUUA AUACCCUGCUCAGAGCCCUUCCUCCCUAGCUUCCGCUUGUA AGACGGGGAAAUCAGGAAGGUCAAACCAAAUCAAGCUGGCG UGGAUUCCCCCACCUGAGGGAUGAAGCGCGAGAUCUAAUUC AGGUUAGCCAUUCGUUAGCGUGUCGGUUCGCAGGCGGUGGU GAAAUUAAAGAUCGACUAAGCAUGUAGUACCAAAGAUGAAU GGUUUUCGGACGGGGGUUCAACUCCCCCCAGCUCCACCA Yersinia pestis ssrA SEQ ID NO: 129 GGGGCTGATTCTGGATTCGACGGGATTCGCGAAACCCAAGGT GCATGCCGAGGTGCGGTGGCCTCGTAAAAAACCGCAAAAAAA ATAGTTGCAAACGACGAAAACTACGCACTAGCAGCTTAATAA CCTGCTTAGAGCCCTCTCTGCCTAGCCTCCGCTCTTAGGACGG GGATCAAGAGAGGTCAAACCTAAAAGAGCTCGTGTGGAAACC TTGCCTGGGGTGGAAGCATTAAAACTAATCAGGATAGTTTGTC AGTAGCGTGTCCATCCGCAGCTGGCCGGCGAATGTAATGATT GGACTAAGCATGTAGTGCCGACGGTGTAGTAATTTCGGACGG GGGTTCAAATCCCCCCAGCTCCACCA Yersinia pestis tmRNA SEQ ID NO: 130 GGGGCUGAUUCUGGAUUCGACGGGAUUCGCGAAACCCAAGG UGCAUGCCGAGGUGCGGUGGCCUCGUAAAAAACCGCAAAAA AAAUAGUUGCAAACGACGAAAACUACGCACUAGCAGCUUAA UAACCUGCUUAGAGCCCUCUCUGCCUAGCCUCCGCUCUUAG GACGGGGAUCAAGAGAGGUCAAACCUAAAAGAGCUCGUGUG GAAACCUUGCCUGGGGUGGAAGCAUUAAAACUAAUCAGGAU AGUUUGUCAGUAGCGUGUCCAUCCGCAGCUGGCCGGCGAAU GUAAUGAUUGGACUAAGCAUGUAGUGCCGACGGUGUAGUAA UUUCGGACGGGGGUUCAAAUCCCCCCAGCUCCACCA Campylobacter fetus ssrA, internal partial SEQ ID NO: 131 AGGAGTAAGTCTGCTTAGATGGCATGTCGCTTTGGGCAAAGC GTAAAAAGCCCAAATAAAATTAAACGCAAACAACGTTAAATT CGCTCCTGCTTACGCTAAAGCTGCGTAAGTTCAGTTGAGCCTG AAATTTAAGTCATACTATCTAGCTTAATTTTCGGTCATCTTTGA TAGTGTAGCCTTGCGTTTGACAAGCGTTGAGGTGAAATAAAGT CTTAGCCTTGCTTTTGAGTTTTGGAAGATGAGCGAAGTAGGGT GAAGTAGTCATCTTTGCTAAGCATGTAGAGGTCTTTGTGGGAT TATTTTTGG Campylobacter fetus tmRNA, internal partial SEQ ID NO: 132 AGGAGUAAGUCUGCUUAGAUGGCAUGUCGCUUUGGGCAAAG CGUAAAAAGCCCAAAUAAAAUUAAACGCAAACAACGUUAAA UUCGCUCCUGCUUACGCUAAAGCUGCGUAAGUUCAGUUGAG CCUGAAAUUUAAGUCAUACUAUCUAGCUUAAUUUUCGGUCA UCUUUGAUAGUGUAGCCUUGCGUUUGACAAGCGUUGAGGUG AAAUAAAGUCUUAGCCUUGCUUUUGAGUUUUGGAAGAUGA GCGAAGUAGGGUGAAGUAGUCAUCUUUGCUAAGCAUGUAGA GGUCUUUGUGGGAUUAUUUUUGG Campylobacter coli (BM2509) ssrA, internal partial SEQ ID NO: 133 AGGAGTAAGTCTGCTTAGATGGCATGTCGCTTTGGACAAAGC GTAAAAAGTCCAAATTAAAATTAAACGCAAATAACGTTAAAT TTGCTCCTGCTTACGCTAAAGCTGCGTAAGTTCAGTTGAGCCC GAAACTCAAGTGATGCTATCTAGCTTGAATTTTGGTCATCTTT GATAGTGTAGATTGAAAATTGACAACTTTTAATCGAAGTTAAA GTCTTAGTCTAGCTTGAAATTTTGGAAGGTGAGTTTAGCCAGA TGAAGTTTTCACCTTTGCTAAACATGTAGAAGTCTTTGTGGGG TTATTTTTGG Campylobacter coli (BM2509) tmRNA, internal partial SEQ ID NO: 134 AGGAGUAAGUCUGCUUAGAUGGCAUGUCGCUUUGGACAAAG CGUAAAAAGUCCAAAUUAAAAUUAAACGCAAAUAACGUUAA AUUUGCUCCUGCUUACGCUAAAGCUGCGUAAGUUCAGUUGA GCCCGAAACUCAAGUGAUGCUAUCUAGCUUGAAUUUUGGUC AUCUUUGAUAGUGUAGAUUGAAAAUUGACAACUUUUAAUC GAAGUUAAAGUCUUAGUCUAGCUUGAAAUUUUGGAAGGUG AGUUUAGCCAGAUGAAGUUUUCACCUUUGCUAAACAUGUAG AAGUCUUUGUGGGGUUAUUUUUGG Camplyobacter chicken isolate ssrA, internal partial SEQ ID NO: 135 ACAGGAGTAAGTCTGCTTAGATGGCATGTCGCTTTGGGCAAA GCGTAAAAAGCCCAAATAAAATTAAACGCAAACAACGTTAAA TTCGCTCCTGCTTACGCTAAAGCTGCGTAAGTTCAGTTGAGCC TGAAATTTAAGTCATACTATCTAGCTTAATTTTCGGTCATTTTT GATAGTGTAGCCTTGCGTTTGACAAGCGTTGAGGTGAAATAA GGTCTTAGCCTTGCTTTTGAGTTTTGGAAGATGAGCGAAGTAG GGTGAAGTAGTCATCTTTGCTAAGCATGTAGAGGTCTTTGTGG GATTATTTTTGG Camplyobacter chicken isolate tmRNA, internal partial SEQ ID NO: 136 ACAGGAGUAAGUCUGCUUAGAUGGCAUGUCGCUUUGGGCAA AGCGUAAAAAGCCCAAAUAAAAUUAAACGCAAACAACGUUA AAUUCGCUCCUGCUUACGCUAAAGCUGCGUAAGUUCAGUUG AGCCUGAAAUUUAAGUCAUACUAUCUAGCUUAAUUUUCGGU CAUUUUUGAUAGUGUAGCCUUGCGUUUGACAAGCGUUGAGG UGAAAUAAGGUCUUAGCCUUGCUUUUGAGUUUUGGAAGAU GAGCGAAGUAGGGUGAAGUAGUCAUCUUUGCUAAGCAUGUA GAGGUCUUUGUGGGAUUAUUUUUGG Clostridium perfringens ssrA, internal partial SEQ ID NO: 137 ACGGGGGTAGGATGGGTTTGATAAGCGAGTCGAGGGAAGCAT GGTGCCTCGATAATAAAGTATGCATTAAAGATAAACGCACGA GATAATTTTGCATTAGCAGCTTAAGTTAGCGCTGCTCATCCTT CCTCAATTGCCCACGGTTGAGAGTAAGGGTGTCATTTAAAAGT GGGGAACCGAGCCTAGCAAAGCTTTGAGCTAGGAACGGAATT TATGAAGCTTACCAAAGAGGAAGTTTGTCTGTGGACGTTCTCT GAGGGAATTTTAAAACACAAGACTACACTCGTAGAAAGTCTT ACTGGTCTGCTTTCGG Clostridium perfringens tmRNA, internal partial SEQ ID NO: 138 ACGGGGGUAGGAUGGGUUUGAUAAGCGAGUCGAGGGAAGC AUGGUGCCUCGAUAAUAAAGUAUGCAUUAAAGAUAAACGCA CGAGAUAAUUUUGCAUUAGCAGCUUAAGUUAGCGCUGCUCA UCCUUCCUCAAUUGCCCACGGUUGAGAGUAAGGGUGUCAUU UAAAAGUGGGGAACCGAGCCUAGCAAAGCUUUGAGCUAGGA ACGGAAUUUAUGAAGCUUACCAAAGAGGAAGUUUGUCUGUG GACGUUCUCUGAGGGAAUUUUAAAACACAAGACUACACUCG UAGAAAGUCUUACUGGUCUGCUUUCGG Haemophilus ducreyi (NCTC 10945) ssrA, internal partial SEQ ID NO: 139 ACGGGATTAGCGAAGTCCAAGGTGCACGTCGAGGTGCGGTAG GCCTCGTAACAAACCGCAAAAAAATAGTCGCAAACGACGAAC AATACGCTTTAGCAGCTTAATAACCTGCATTTAGCCTTCGCGC CCTAGCTTTCGCTCGTAAGACGGGGAGCACGCGGAGTCAAAC CAAAACGAGATCGTGTGGACGCTTCCGCTTGTAGATGAAACA CTAAATTGAATCAAGCTAGTTTATTTCTTGCGTGTCTGTCCGCT GGAGATAAGCGAAATTAAAGACCAGACTAAACGTGTAGTACT GAAGATAGAGTAATTTCGGACCCGGGTTCGACTC Haemophilus ducreyi (NCTC 10945) tmRNA, internal partial SEQ ID NO: 140 ACGGGAUUAGCGAAGUCCAAGGUGCACGUCGAGGUGCGGUA GGCCUCGUAACAAACCGCAAAAAAAUAGUCGCAAACGACGA ACAAUACGCUUUAGCAGCUUAAUAACCUGCAUUUAGCCUUC GCGCCCUAGCUUUCGCUCGUAAGACGGGGAGCACGCGGAGU CAAACCAAAACGAGAUCGUGUGGACGCUUCCGCUUGUAGAU GAAACACUAAAUUGAAUCAAGCUAGUUUAUUUCUUGCGUGU CUGUCCGCUGGAGAUAAGCGAAAUUAAAGACCAGACUAAAC GUGUAGUACUGAAGAUAGAGUAAUUUCGGACCCGGGUUCGA CUC Listeria innocua (food isolate #1) ssrA, internal partial SEQ ID NO: 141 GGCAAAGAAAAACAAAACCTAGCTTTCGCTGCCTAATAACCA GTAGCATAGCTGATCCTCCGTGCATCGCCCATGTGCTACGGTA AGGGTCTCACTCTAAGTGGGCTACACTAGTTAATCTCCGTCTG AGGTTAAATAGAAGAGCTTAATCAGACTAGCTGAATGGAAGC CTGTTACCGGGCTGATGTTTATGCGAAATGCTAATACGGTGAC TACGCTCGTAGATATTCAA Listeria innocua (food isolate #1) tmRNA, internal partial SEQ ID NO: 142 GGCAAAGAAAAACAAAACCUAGCUUUCGCUGCCUAAUAACC AGUAGCAUAGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACG GUAAGGGUCUCACUCUAAGUGGGCUACACUAGUUAAUCUCC GUCUGAGGUUAAAUAGAAGAGCUUAAUCAGACUAGCUGAAU GGAAGCCUGUUACCGGGCUGAUGUUUAUGCGAAAUGCUAAU ACGGUGACUACGCUCGUAGAUAUUCAA Listeria innocua (food isolate #2) ssrA, internal partial SEQ ID NO: 143 GGCAAAGAAAAACAAAACCTAGCTTTCGCTGCCTAATAAGCA GTAGCATAGCTGATCCTCCGTGCATCGCCCATGTGCTACGGTA AGGGTCTCACTCTAAGTGGGCTACACTAGTTAATCTCCGTCTG AGGTTAAATAGAAGAGCTTAATCAGACTAGCTGAATGGAAGC CTGTTACCGGGCCGATGTTTATGCGAAATGCTAATACGGTGAC TACGCTCGTAGATATTTAA Listeria innocua (food isolate #2) tmRNA, internal partial SEQ ID NO: 144 GGCAAAGAAAAACAAAACCUAGCUUUCGCUGCCUAAUAAGC AGUAGCAUAGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACG GUAAGGGUCUCACUCUAAGUGGGCUACACUAGUUAAUCUCC GUCUGAGGUUAAAUAGAAGAGCUUAAUCAGACUAGCUGAAU GGAAGCCUGUUACCGGGCCGAUGUUUAUGCGAAAUGCUAAU ACGGUGACUACGCUCGUAGAUAUUUAA Listeria innocua (food isolate #3) ssrA, internal partial SEQ ID NO: 145 GGCAAAGAAAAACAAAACCTAGCTTTCGCTGCCTAATAAGCA GTAGAATAGCTGATCCTCCGTGCATCGCCCATGTGCTACGGTA AGGGTCTCACTCTAAGTGGGCTACACTAGTTAATCTCCGTCTG AGGTTAAATAGAAGAGCTTAATCGGACTAGCTGAATGGAAGC CTGTTACCGGGCCGATGTTTATGCGAAATGCTAATACGGTGAC TACGCTCGTAGATATTTAA Listeria innocua (food isolate #3) tmRNA, internal partial SEQ ID NO: 146 GGCAAAGAAAAACAAAACCUAGCUUUCGCUGCCUAAUAAGC AGUAGAAUAGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACG GUAAGGGUCUCACUCUAAGUGGGCUACACUAGUUAAUCUCC GUCUGAGGUUAAAUAGAAGAGCUUAAUCGGACUAGCUGAAU GGAAGCCUGUUACCGGGCCGAUGUUUAUGCGAAAUGCUAAU ACGGUGACUACGCUCGUAGAUAUUUAA Listeria innocua (ATCC 12210) ssrA, internal partial SEQ ID NO: 147 GGCAAAGAAAAACAAAACCTAGCTTTCGCTGCCTAATAAGCA GTAGCATAGCTGATCCTCCGTGCATCGCCCATGTGCTACGGTA AGGGTCTCACTCTAAGTGGGCTACACTAGTTAATCTCCGTCTG GGGTTAAATAGAAGAGCTTAATCAGACTAGCTGAATGGAAGC CTGTTACTGGGCCGATGTTTATGCGAAATGCTAATACGGTGAC TACGCTCGTAGATATTTAA Listeria innocua (ATCC 12210) tmRNA, internal partial SEQ ID NO: 148 GGCAAAGAAAAACAAAACCUAGCUUUCGCUGCCUAAUAAGC AGUAGCAUAGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACG GUAAGGGUCUCACUCUAAGUGGGCUACACUAGUUAAUCUCC GUCUGGGGUUAAAUAGAAGAGCUUAAUCAGACUAGCUGAAU GGAAGCCUGUUACUGGGCCGAUGUUUAUGCGAAAUGCUAAU ACGGUGACUACGCUCGUAGAUAUUUAA Listeria ivanovii (NCTC 11846) ssrA, internal partial SEQ ID NO: 149 ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGT CCTCGTTATTAACGTCAAAGCCAATAATAACTGGCAAAGAAA AACAAAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCT GATCCTCCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACT TTAAGTGGGCTACACTAAATAATCTCCGTCTGGGGTTAGTTAG AAGAGCTTAATCAGACTAGCTGAATGGAAGCCTGTTACCGGG CTGATGTTTATGCGAAATGCTAATACGGTGACTACGCTCGTAG ATATTTAAGTGCCGATATTTCTGG Listeria ivanovii (NCTC 11846) tmRNA, internal partial SEQ ID NO: 150 ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCG UCCUCGUUAUUAACGUCAAAGCCAAUAAUAACUGGCAAAGA AAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAU AGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGU CUCACUUUAAGUGGGCUACACUAAAUAAUCUCCGUCUGGGG UUAGUUAGAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCU GUUACCGGGCUGAUGUUUAUGCGAAAUGCUAAUACGGUGAC UCGCUCGUAGAUAUUUAAGUGCCGAUAUUUCUGG Listeria seeligeri (NCTC 11856) ssrA, internal partial SEQ ID NO: 151 ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGT CCTCGTTATCAACGTCAAAGCCAATAATAACTGGCAAAGAAA AACAAAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCT GATCCTCCGTGCATCGCCCATGTGCTACGGAAAGGGTCTCACT TTAAGTGGGCTACACTAAATAATCTCCGTCTGGGGTTAGTTAG AAGAGCTTAATCAGACTAGCTGAATGGAAGCCTGTTACCGGG CTGATGTTTATGCGAAATACTAATACGGTGACTACGCTCGTAG ATATTTAAGTGCCCATATTTCTGG Listeria seeligeri (NCTC 11856) tmRNA, internal partial SEQ ID NO: 152 ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCG UCCUCGUUAUCAACGUCAAAGCCAAUAAUAACUGGCAAAGA AAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAU AGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGAAAGGGU CUCACUUUAAGUGGGCUACACUAAAUAAUCUCCGUCUGGGG UUAGUUAGAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCU GUUACCGGGCUGAUGUUUAUGCGAAAUACUAAUACGGUGAC UACGCUCGUAGAUAUUUAAGUGCCCAUAUUUCUGG Salmonella enteritidis ssrA, internal partial SEQ ID NO: 153 ACGGGATTTGCGAAACCCAAGGTGCATGCCGAGGGGCGGTTG GCCTCGTAAAAAGCCGCAAAAAAATAGTCGCAAACGACGAAA CCTACGCTTTAGCAGCTTAATAACCTGCTTAGAGCCCTCTCTC CCTAGCCTCCGCTCTTAGGACGGGGATCAAGAGAGGTCAAAC CCAAAAGAGATCGCGTGGATGCCCTGCCTGGGGTTGAAGCGT TAAAACGAATCAGGCTAGTCTGGTAGTGGCGTGTCCGTCCGC AGGTGCCAGGCGAATGTAAAGACTGACTAAGCATGTAGTACC GAGGATGTAGGAATTTCGG Salmonella enteritidis tmRNA, internal partial SEQ ID NO: 154 ACGGGAUUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUU GGCCUCGUAAAAAGCCGCAAAAAAAUAGUCGCAAACGACGA AACCUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUC UCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGU CAAACCCAAAAGAGAUCGCGUGGAUGCCCUGCCUGGGGUUG AAGCGUUAAAACGAAUCAGGCUAGUCUGGUAGUGGCGUGUC CGUCCGCAGGUGCCAGGCGAAUGUAAAGACUGACUAAGCAU GUAGUACCGAGGAUGUAGGAAUUUCGG Staphylococcus epidermidis (NCTC 11047) ssrA, internal partial SEQ ID NO: 155 ACAGGGGTCCCCCGAGCTTATTAAGCGTGTCGGAGGGTTGGC TCCGTCATCAACACATTTCGGTTAAATATAACTGACAAATCAA ACAATAATTTCGCAGTAGCTGCGTAATAGCCACTGCATCGCCT AACAGCATCTCCTACGTGCTGTTAACGCGATTCAACCCTAGTA GGATATGCTAAACACTGCCGCTTGAAGTCTGTTTAGATGAAAT ATAATCAAGCTAGTATCATGTTGGTTGTTTATTGCTTAGCATG ATGCGAAAATTATCAATAAACTACACACGTAGAAAGATTTGT ATCAGGACCTCTGG Staphylococcus epidermidis (NCTC 11047) tmRNA, internal partial SEQ ID NO: 156 ACAGGGGUCCCCCGAGCUUAUUAAGCGUGUCGGAGGGUUGG CUCCGUCAUCAACACAUUUCGGUUAAAUAUAACUGACAAAU CAAACAAUAAUUUCGCAGUAGCUGCGUAAUAGCCACUGCAU CGCCUAACAGCAUCUCCUACGUGCUGUUAACGCGAUUCAAC CCUAGUAGGAUAUGCUAAACACUGCCGCUUGAAGUCUGUUU AGAUGAAAUAUAAUCAAGCUAGUAUCAUGUUGGUUGUUUA UUGCUUAGCAUGAUGCGAAAAUUAUCAAUAAACUACACACG UAGAAAGAUUUGUAUCAGGACCUCUGG Streptococcus agalactiae (NCTC 8181) ssrA, internal partial SEQ ID NO: 157 ACAGGCATTATGAGGTATATTTTGCGACTCATCGGCAGATGTA AAATGCCAGTTAAATATAACTGCAAAAAATACAAATTCTTAC GCATTAGCTGCCTAAAAAACAGCCTGCGTGATCTTCACAAGAT TGTTTGCGTTTTGCTAGAAGGTCTTATTTATCAGCAAACTACG TTTGGCTACTGTCTAGTTAGTTAAAAAGAGATTTATAGACTCG CTATGTGAGGGCTTGAGTTATGTGTCATCACCTAGTTAAATCA ATACATAACCTATAGTTGTAGACAAATATATTAGCAGATGTTT GG Streptococcus agalactiae (NCTC 8181) tmRNA, internal partial SEQ ID NO: 158 ACAGGCAUUAUGAGGUAUAUUUUGCGACUCAUCGGCAGAUG UAAAAUGCCAGUUAAAUAUAACUGCAAAAAAUACAAAUUCU UACGCAUUAGCUGCCUAAAAAACAGCCUGCGUGAUCUUCAC AAGAUUGUUUGCGUUUUGCUAGAAGGUCUUAUUUAUCAGCA AACUACGUUUGGCUACUGUCUAGUUAGUUAAAAAGAGAUUU AUAGACUCGCUAUGUGAGGGCUUGAGUUAUGUGUCAUCACC UAGUUAAAUCAAUACAUAACCUAUAGUUGUAGACAAAUAUA UUAGCAGAUGUUUGG Bordetella bronchiseptica ssrA SEQ ID NO: 159 GGGGCCGATCCGGATTCGACGTGGGTCATGAAACAGCTCAAG GCATGCCGAGCACCAGTAAGCTCGTTAATCCACTGGAACACT ACAAACGCCAACGACGAGCGTTTCGCTCTCGCCGCTTAAGCG GTGAGCCGCTGCACTGATCTGTCCTTGGGTCACGCGGGGGAA Bordetella bronchiseptica tmRNA SEQ ID NO: 160 GGGGCCGAUCCGGAUUCGACGUGGGUCAUGAAACAGCUCAAG GCAUGCCGAGCACCAGUAAGCUCGUUAAUCCACUGGAACACU ACAAACGCCAACGACGAGCGUUUCGCUCUCGCCGCUUAAGCG GUGAGCCGCUGCACUGAUCUGUCCUUGGGUCACGCGGGGGAA Chlamydia pneumoniae (CWL029), ssrA SEQ ID NO: 161 GGGGGTGTATAGGTTTCGACTTGAAAATGAAGTGTTAATTGCA TGCGGAGGGCGTTGGCTGGCCTCCTAAAAAGCCAACAAAACA ATAAATGCCGAACCTAAGGCTGAATGCGAAATTATTAGCTTGT TTGACTCAGTAGAGGAAAGACTAGCTGCTTAATTAGCAAAAG TTGTTAGCTAGATAATCTCTAGGTAACCCGGTATCTGCGAGCT CCACCAGAGGCTTGCAAAATACCGTCATTTATCTGGTTGGAAC TTACTTTCTCTAATTCTCAAGGAAGTTCGTTCGAGATTTTTGAG AGTCATTGGCTGCTATAGAGGCTTCTAGCTAAGGGAGTCCAAT GTAAACAATTCTAGAAGATAAGCATGTAGAGGTTAGCAGGGA GTTTGTCAAGGACGAGAGTTCGAGTCTCTCCACCTCCACCA Chlamydia pneumoniae (CWL029) tmRNA SEQ ID NO: 162 GGGGGUGUAUAGGUUUCGACUUGAAAAUGAAGUGUUAAUU GCAUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCAACAA AACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUUA GCUUGUUUGACUCAGUAGAGGAAAGACUAGCUGCUUAAUUA GCAAAAGUUGUUAGCUAGAUAAUCUCUAGGUAACCCGGUAU CUGCGAGCUCCACCAGAGGCUUGCAAAAUACCGUCAUUUAU CUGGUUGGAACUUACUUUCUCUAAUUCUCAAGGAAGUUCGU UCGAGAUUUUUGAGAGUCAUUGGCUGCUAUAGAGGCUUCUA GCUAAGGGAGUCCAAUGUAAACAAUUCUAGAAGAUAAGCAU GUAGAGGUUAGCAGGGAGUUUGUCAAGGACGAGAGUUCGA GUCUCUCCACCUCCACCA Francisella tularensis ssrA SEQ ID NO: 163 GGGGGCGAATATGGTTTCGACATGAATGTCAAAATCTAAGGT GCATGCCGAGGAAGTACCGTAACCTCGTTAATAACAGTACAA ATGCCAATAATAACTGGCAACAAAAAAGCAAACCGCGTAGCG GCTAACGACAGCAACTTTGCTGCTGTTGCTAAAGCTGCCTAGT CTAGCTTAATAATCTAGATGCGCACGGATATGATAGTCTTTCT TATGACACTATCTATACATCCGTTCATATTCCGCATAAGACGG TCTTTGCTTTTTGTCTGGGAGTTAAGGCTGTATTTAACAGACTC GCTAACTATTACCCTGGCTAATTGGGGAATAGTCAAGCTAAAC TCAAATAGATTAGCCTAAGCATGTAGATCCAAAGATCTAGAG TTTGTGGACGCGGGTTCAAATCCCGCCGCCTCCACCA Francisella tularensis tmRNA SEQ ID NO: 164 GGGGGCGAAUAUGGUUUCGACAUGAAUGUCAAAAUCUAAGG UGCAUGCCGAGGAAGUACCGUAACCUCGUUAAUAACAGUAC AAAUGCCAAUAAUAACUGGCAACAAAAAAGCAAACCGCGUA GCGGCUAACGACAGCAACUUUGCUGCUGUUGCUAAAGCUGC CUAGUCUAGCUUAAUAAUCUAGAUGCGCACGGAUAUGAUAG UCUUUCUUAUGACACUAUCUAUACAUCCGUUCAUAUUCCGC AUAAGACGGUCUUUGCUUUUUGUCUGGGAGUUAAGGCUGUA UUUAACAGACUCGCUAACUAUUACCCUGGCUAAUUGGGGAA UAGUCAAGCUAAACUCAAAUAGAUUAGCCUAAGCAUGUAGA UCCAAAGAUCUAGAGUUUGUGGACGCGGGUUCAAAUCCCGC CGCCUCCACCA Guillardia theta (plastid) ssrA SEQ ID NO: 165 GGGGCTGATTTGGATTCGACATATAAATTTGCGTGTTTCATTA TGAAGCAAGTCAAGTTTAATGATCTTGTAAAAAACATTAAAG TACAAATAAATGCAAGCAATATAGTTTCATTTAGTTCAAAACG TTTAGTCTCTTTTGCATAAGCAAAATGTGTTAATAACTTTCTTA GTAGAAATTGGAGAAGTTTACTAAGATTTATATTTACTCCATA ATTATTTTAAAGATGGTAAAAAGGTGATTCATCATTTGTATGT TTCTAAACTTTGTGAAAGAATAGTGGGCTCCATTTATAATGAA CGTGGGTTCAAATCCCACCAGCTCCACCA Guillardia theta (plastid) tmRNA SEQ ID NO: 166 GGGGCUGAUUUGGAUUCGACAUAUAAAUUUGCGUGUUUCAU UAUGAAGCAAGUCAAGUUUAAUGAUCUUGUAAAAAACAUU AAAGUACAAAUAAAUGCAAGCAAUAUAGUUUCAUUUAGUUC AAAACGUUUAGUCUCUUUUGCAUAAGCAAAAUGUGUUAAUA ACUUUCUUAGUAGAAAUUGGAGAAGUUUACUAAGAUUUAU AUUUACUCCAUAAUUAUUUUAAAGAUGGUAAAAAGGUGAU UCAUCAUUUGUAUGUUUCUAAACUUUGUGAAAGAAUAGUG GGCUCCAUUUAUAAUGAACGUGGGUUCAAAUCCCACCAGCU CCACCA Thalassiosira Weissflogii (plastid) ssrA SEQ ID NO: 167 GGGGCTGATTTGGTTTCGACATTTAAAACTTCTTTCTATGTGTC AGGTCAAAGTTTGTATTCTTTGTAAAAAAATACTAAAATACTA ATAAATGCTAATAATATAATACCGTTTATTTTTAAAGCAGTAA AAACAAAAAAAGAAGCAATGGCTTTAAATTTTGCTGTATAGT TCATTAACTTAGGTTATTAAATATTTTTTCATTATAACTGGACT TTTCTCTAGTTTATAGTTTAGAATAAATTTAAATTTTGCAAAAC TCGTTCGAAAATTTTCGGGCTAAACCTGTAAACGCAAATACTA AGAAATTTTAGATGGACATGGGTTCAATTCCCATCAGTTCCAC CA Thalassiosira Weissflogii (plastid) tmRNA SEQ ID NO: 168 GGGGCUGAUUUGGUUUCGACAUUUAAAACUUCUUUCUAUGU GUCAGGUCAAAGUUUGUAUUCUUUGUAAAAAAAUACUAAA AUACUAAUAAAUGCUAAUAAUAUAAUACCGUUUAUUUUUA AAGCAGUAAAAACAAAAAAAGAAGCAAUGGCUUUAAAUUU UGCUGUAUAGUUCAUUAACUUAGGUUAUUAAAUAUUUUUU CAUUAUAACUGGACUUUUCUCUAGUUUAUAGUUUAGAAUAA AUUUAAAUUUUGCAAAACUCGUUCGAAAAUUUUCGGGCUAA ACCUGUAAACGCAAAUACUAAGAAAUUUUAGAUGGACAUGG GUUCAAUUCCCAUCAGUUCCACCA Helicobacter pylori ssrA, (clinical isolate 1), internal partial SEQ ID NO: 176 TGGGGATGTTACGGTTTCGACAGGGGTAGTTCGAGCTTAGGTG GCGAGTCGAGGGGATCGGCCTCGTTAAAACGTCAAAGCCTAT AACTGGCAAACAACAAAACAACTTCGCTTTAGCAGCTTAATA AGCTCTTAGCGGTTCCTCCCTCCATCGCCCATGTGGTAGGGTA AGGGACTCAAATTAAGTGGGCTACGCTGGATTCCACCGTCTG AGGATGAAAGAAGAGAACAACCAGACTAGCTACCCGGACGC CCGTCGATAGGCAGATGGAGTAGCGAATCGCGAATATATCGA CTACACTCGTAGAAGCTTAAGTGCCGATATTCTTGGACGTGGG TTCGACTCCC Helicobacter pylori tmRNA, (clinical isolate 1), internal partial SEQ ID NO: 177 UGGGGAUGUUACGGUUUCGACAGGGGUAGUUCGAGCUUAGG UGGCGAGUCGAGGGGAUCGGCCUCGUUAAAACGUCAAAGCC UAUAACUGGCAAACAACAAAACAACUUCGCUUUAGCAGCUU AAUAAGCUCUUAGCGGUUCCUCCCUCCAUCGCCCAUGUGGU AGGGUAAGGGACUCAAAUUAAGUGGGCUACGCUGGAUUCCA CCGUCUGAGGAUGAAAGAAGAGAACAACCAGACUAGCUACC CGGACGCCCGUCGAUAGGCAGAUGGAGUAGCGAAUCGCGAA UAUAUCGACUACACUCGUAGAAGCUUAAGUGCCGAUAUUCU UGGACGUGGGUUCGACUCCC Helicobacter pylori ssrA, (clinical isolate 2), internal partial SEQ ID NO: 178 TGGGGACGTTACGGTTTCGACAGGGATAGTTCGAGCTTAGGTT GCGAGTCGAGGGGATCGGCCTCGTTAAAACGTCAAAGCCTAT AATTGGCAAACAAAACAATCTTTCTTTAGCTGCTTAATTGCAC TAAAGGTTCCTCCCTCCATCGTCCATGTGGTAGGGTAAGGGAC TCAAACTAAGTGGACTACGCCGGAGTTCGCCGTCTGAGGACA AAGGAAGAGAACAACCAGACTAGCAACTTGGAAGCCTGTCGA TAGGCCGAAGAGTTCGCGAAATGCTAATATATCGACTACACT CGTAGAAGCTTAAGTGCCGATATTTTTGGACGTGGGTTCGATT CCCT Helicobacter pylori tmRNA, (clinical isolate 2), internal partial SEQ ID NO: 179 UGGGGACGUUACGGUUUCGACAGGGAUAGUUCGAGCUUAGG UUGCGAGUCGAGGGGAUCGGCCUCGUUAAAACGUCAAAGCC UAUAAUUGGCAAACAAAACAAUCUUUCUUUAGCUGCUUAAU UGCACUAAAGGUUCCUCCCUCCAUCGUCCAUGUGGUAGGGU AAGGGACUCAAACUAAGUGGACUACGCCGGAGUUCGCCGUC UGAGGACAAAGGAAGAGAACAACCAGACUAGCAACUUGGAA GCCUGUCGAUAGGCCGAAGAGUUCGCGAAAUGCUAAUAUAU CGACUACACUCGUAGAAGCUUAAGUGCCGAUAUUUUUGGAC GUGGGUUCGAUUCCCU Listeria seeligeri (NCTC 11856) ssrA, internal partial SEQ ID NO: 180 ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGT CCTCGTTATCAACGTCAAAGCCAATAATAACTGGCAAAGAAA AACAAAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCT GATCCTCCGTGCATCGCCCATGTGCTACGGAAAGGGTCTCACT TTAAGTGGGCTACACTAAATAATCTCCGTCTGGGGTTAGTTAG AAGAGCTTAATCAGACTAGCTGAATGGAAGCCTGTTACCGGG CTGATGTTTATGCGAAATACTAATACGGTGACTACGCTCGTAG ATATTTAAGTGCCCATATTTCTGG Listeria seeligeri (NCTC 11856) tmRNA, internal partial SEQ ID NO: 181 ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCG UCCUCGUUAUCAACGUCAAAGCCAAUAAUAACUGGCAAAGA AAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAU AGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGAAAGGGU CUCACUUUAAGUGGGCUACACUAAAUAAUCUCCGUCUGGGG UUAGUUAGAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCU GUUACCGGGCUGAUGUUUAUGCGAAAUACUAAUACGGUGAC UACGCUCGUAGAUAUUUAAGUGCCCAUAUUUCUGG Listeria ivanovii (NCTC 11846) ssrA, internal partial SEQ ID NO: 182 ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGT CCTCGTTATTAACGTCAAAGCCAATAATAACTGGCAAAGAAA AACAAAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCT GATCCTCCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACT TTAAGTGGGCTACACTAAATAATCTCCGTCTGGGGTTAGTTAG AAGAGCTTAATCAGACTAGCTGAATGGAAGCCTGTTACCGGG CTGATGTTTATGCGAAATGCTAATACGGTGACTACGCTCGTAG ATATTTAAGTGCCGATATTTCTGG Listeria ivanovii (NCTC 11846) tmRNA, internal partial SEQ ID NO: 183 ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCG UCCUCGUUAUUAACGUCAAAGCCAAUAAUAACUGGCAAAGA AAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAU AGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGU CUCACUUUAAGUGGGCUACACUAAAUAAUCUCCGUCUGGGG UUAGUUAGAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCU GUUACCGGGCUGAUGUUUAUGCGAAAUGCUAAUACGGUGAC UCGCUCGUAGAUAUUUAAGUGCCGAUAUUUCUGG Mycobacterium africanum (clinical isolate) ssrA, internal partial SEQ ID NO: 184 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCGACCAAATAAGCGCCGATT CACATCAGCGCGACTACGCTCTCGCTGCCTAAGCGACGGCTA GTCTGTCAGACCGGGAACGCCCTCGGCCCGGACCCTGGCATC AGCTAGAGGGATCCACCGATGAGTCCGGTCGCGGGACTCCTC GGGACAACCACAGCGACTGGGATCGTCATCTCGGCTAGTTCG CGTGACCGGGAGATCCGAGCAGAGGCATAGCGAACTGCGCAC GGAGAAGCCTTGAGGGAATGCCGTA Mycobacterium africanum (clinical isolate) tmRNA, internal partial SEQ ID NO: 185 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCGACCAAAUAAGCGCCGA UUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACGG CUAGUCUGUCAGACCGGGAACGCCCUCGGCCCGGACCCUGG CAUCAGCUAGAGGGAUCCACCGAUGAGUCCGGUCGCGGGAC UCCUCGGGACAACCACAGCGACUGGGAUCGUCAUCUCGGCU AGUUCGCGUGACCGGGAGAUCCGAGCAGAGGCAUAGCGAAC UGCGCACGGAGAAGCCUUGAGGGAAUGCCGUA Mycobacterium gordonae (clinical isolate) ssrA, internal partial SEQ ID NO: 186 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCAACCATATAAGCGCCGATT CACATCAGCGCGACTACGCTCTCGCTGCCTAAGCGACGGCTA GTCTGTCGGACCGGGAACGCCCTCGCCCCGGACCCCGGCATC AGCTAGAGGGATCAACCGATGAGTTCGGTCGCGGGACTCATC GGGACACCAACAGCGACTGGGATCGTCATCCTGGCTAGTCCG TGTGACCAGGAGATCCGAGCAGAGACATAGCGGACTGCGCAC GGAGAAGCCTTGAGGGAATGCCGTA Mycobacterium gordonae (clinical isolate) tmRNA, internal partial SEQ ID NO: 187 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCAACCAUAUAAGCGCCGA UUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACGG CUAGUCUGUCGGACCGGGAACGCCCUCGCCCCGGACCCCGGC AUCAGCUAGAGGGAUCAACCGAUGAGUUCGGUCGCGGGACU CAUCGGGACACCAACAGCGACUGGGAUCGUCAUCCUGGCUA GUCCGUGUGACCAGGAGAUCCGAGCAGAGACAUAGCGGACU GCGCACGGAGAAGCCUUGAGGGAAUGCCGUA Mycobacterium kansasii (clinical isolate) ssrA, internal partial SEQ ID NO: 188 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCAACCAAATAAGCGCCGATT CACATCAGCGCGACTACGCTCTCGCTGCCTAAGCGACGGCTA GTCTGTCAGACCGGGACCGCCCTCGACCCGGACTCTGGCATCA GCTAGAGGGATCAACCGATGAGTTCGGTCGCGGGACTCGTCG GGACACCAACAGCGACTGGGATCGTCATCCTGGCTAGTTCGC GTGACCAGGAGATCCGAGCAGAGGCATAGCGAACTGCGCACG GAGAAGCCTTGAGGGAATGCCGTA Mycobacterium kansasii (clinical isolate) tmRNA, internal partial SEQ ID NO: 189 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCAACCAAAUAAGCGCCGA UUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACGG CUAGUCUGUCAGACCGGGACCGCCCUCGACCCGGACUCUGG CAUCAGCUAGAGGGAUCAACCGAUGAGUUCGGUCGCGGGAC UCGUCGGGACACCAACAGCGACUGGGAUCGUCAUCCUGGCU AGUUCGCGUGACCAGGAGAUCCGAGCAGAGGCAUAGCGAAC UGCGCACGGAGAAGCCUUGAGGGAAUGCCGUA Mycobacterium chelonae ssrA, internal partial SEQ ID NO: 190 ACAGCGAGTCTCGACTTAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCATTGCAACCAATTAAGCGCCGATT CTCATCAGCGCGACTACGCACTCGCTGCCTAAGCGACTGCGTG TCTGTCAGACCGGGAGCGCCCTCAGCCCGGACCCTGGCATCA GCTAGAGGGACAAACTACGGGTTCGGTCGCGGGACCCGTAGG GACATCAAACAGCGACTGGGATCGTCATCTCGGCTTGTTCGCG GGACCGAGAGATCCAAGTAGAGGCATAGCGAACTGCGCACGG AGAAGCCTTAATGAACGGCCGTTG Mycobacterium chelonae tmRNA, internal partial SEQ ID NO: 191 ACAGCGAGUCUCGACUUAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCAUUGCAACCAAUUAAGCGCCGA UUCUCAUCAGCGCGACUACGCACUCGCUGCCUAAGCGACUG CGUGUCUGUCAGACCGGGAGCGCCCUCAGCCCGGACCCUGG CAUCAGCUAGAGGGACAAACUACGGGUUCGGUCGCGGGACC CGUAGGGACAUCAAACAGCGACUGGGAUCGUCAUCUCGGCU UGUUCGCGGGACCGAGAGAUCCAAGUAGAGGCAUAGCGAAC UGCGCACGGAGAAGCCUUAAUGAACGGCCGUUG Mycobacterium szulgai (ATCC 35799) ssrA, internal partial SEQ ID NO: 192 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCAACCAATTAAGCGCCGAGA ACACTCAGCGCGACTTCGCTCTCGCTGCCTAAGCGACAGCAA GTCCGTCAGACCGGGAAAGCCCTCGACCCGGACCCTGGCGTC ATCTAGAGGGATCCACCGGTGAGTTCGGTCGCGGGACTCATC GGGACACCAACAGCGACTGGGATCGTCATCCTGGCTAGTTCG CGTGACCAGGAGATCCGAGTAGAGACATAGCGAACTGCGCAC GGAGAAGCCTTGAGGGAATGCCGTAG Mycobacterium szulgai (ATCC 35799) tmRNA, internal partial SEQ ID NO: 193 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCAACCAAUUAAGCGCCGA GAACACUCAGCGCGACUUCGCUCUCGCUGCCUAAGCGACAG CAAGUCCGUCAGACCGGGAAAGCCCUCGACCCGGACCCUGG CGUCAUCUAGAGGGAUCCACCGGUGAGUUCGGUCGCGGGAC UCAUCGGGACACCAACAGCGACUGGGAUCGUCAUCCUGGCU AGUUCGCGUGACCAGGAGAUCCGAGUAGAGACAUAGCGAAC UGCGCACGGAGAAGCCUUGAGGGAAUGCCGUAG Mycobacterium malmoense (clinical isolate) ssrA, internal partial SEQ ID NO: 194 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCAACCATATAAGCGCCGTTTC AACACAGCGCGACTACGCTCTCGCTGCCTAAGCGACAGCTAG TCCGTCAGACCGGGAACGCCCTCGACCCGGAGCCTGGCGTCA GCTGGAGGGATCCACCGGTGAGTCCGGTCGCGGGACTCATCG GGACATACACAGCGACTGGGATCGTCATCCTGGCTGGTTCGC GTGACCGGGAGATCCGAGCAGAGGCATAGCGAACTGCGCACG GAGAAGCCTTGAGGGAATGCCGTAG Mycobacterium malmoense (clinical isolate) tmRNA, internal partial SEQ ID NO: 195 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCAACCAUAUAAGCGCCGU UUCAACACAGCGCGACUACGCUCUCGCUGCCUAAGCGACAG CUAGUCCGUCAGACCGGGAACGCCCUCGACCCGGAGCCUGG CGUCAGCUGGAGGGAUCCACCGGUGAGUCCGGUCGCGGGAC UCAUCGGGACAUACACAGCGACUGGGAUCGUCAUCCUGGCU GGUUCGCGUGACCGGGAGAUCCGAGCAGAGGCAUAGCGAAC UGCGCACGGAGAAGCCUUGAGGGAAUGCCGUAG Mycobacterium flavescens ssrA, internal partial SEQ ID NO: 196 ACTTCGAGCGTCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCAACCAATTAAGCGCCGATT CCAATCAGCGCGACTACGCACTCGCTGCCTAAGCGACTGCGT GTCTGTCAGCCCGGGAGAGCCCTCGACCCGGTGTCTGGCATCA GCTAGAGGGATAAACCGGTGGGTCCGGTCGCGGGACTCATCG GGACATCAAACAGCGACTGGGATCGTCATCCTGACTTGTTCGC GTGATCAGGAGATCCGAGTAGAGACATAGCGAACTGCGCACG GAGAAGCCTTGAGGGAACGCCGTAG Mycobacterium flavescens tmRNA, internal partial SEQ ID NO: 197 ACUUCGAGCGUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCAACCAAUUAAGCGCCGA UUCCAAUCAGCGCGACUACGCACUCGCUGCCUAAGCGACUG CGUGUCUGUCAGCCCGGGAGAGCCCUCGACCCGGUGUCUGG CAUCAGCUAGAGGGAUAAACCGGUGGGUCCGGUCGCGGGAC UCAUCGGGACAUCAAACAGCGACUGGGAUCGUCAUCCUGAC UUGUUCGCGUGAUCAGGAGAUCCGAGUAGAGACAUAGCGAA CUGCGCACGGAGAAGCCUUGAGGGAACGCCGUAG Mycobacterium marinum ssrA, internal partial SEQ ID NO: 198 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGATGCAACTAGATAAGCGCCGATT CACATCAGCGCGACTACGCTCTCGCTGCCTAAGCGACGGCTA GTCTGTCGGACCGGGAACGCCCTCGCCCCGGACCCCGGCATC AGCTAGAGGGATCAACCGATGAGTTCGGTCGCGGGGCTCATC GGGACATCAACAGCGACTGGGATCGTCATCCTGGCTAGTTCG CGTGACCAGGAGATCCGAGCAGAGACCTAGCGGACTGCGCAC GGAGAAGCCTTGAGGGAATGCCGTAG Mycobacterium marinum tmRNA, internal partial SEQ ID NO: 199 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGAUGCAACUAGAUAAGCGCCGA UUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACGG CUAGUCUGUCGGACCGGGAACGCCCUCGCCCCGGACCCCGGC AUCAGCUAGAGGGAUCAACCGAUGAGUUCGGUCGCGGGGCU CAUCGGGACAUCAACAGCGACUGGGAUCGUCAUCCUGGCUA GUUCGCGUGACCAGGAGAUCCGAGCAGAGACCUAGCGGACU GCGCACGGAGAAGCCUUGAGGGAAUGCCGUAG Mycobacterium microti (environmental isolate) ssrA, internal partial SEQ ID NO: 200 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCGACCAAATAAGCGCCGATT CACATCAGCGCGACTACGCTCTCGCTGCCTAAGCGACGGCTA GTCTGTCAGACCGGGAACGCCCTCGGCCCGGACCCTGGCATC AGCTAGAGGGATCCACCGATGAGTCCGGTCGCGGGACTCCTC GGGACAGCCACAGCGACTGGGATCGTCATCTCGGCTAGTTCG CGTGACCGGGAGATCCGAGCAGAGGCATAGCGAACTGCGCAC GGAGAAGCCTTGAGGGAATGCCGTA Mycobacterium microti (environmental isolate) tmRNA, internal partial SEQ ID NO: 201 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCGACCAAAUAAGCGCCGA UUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACGG CUAGUCUGUCAGACCGGGAACGCCCUCGGCCCGGACCCUGG CAUCAGCUAGAGGGAUCCACCGAUGAGUCCGGUCGCGGGAC UCCUCGGGACAGCCACAGCGACUGGGAUCGUCAUCUCGGCU AGUUCGCGUGACCGGGAGAUCCGAGCAGAGGCAUAGCGAAC UGCGCACGGAGAAGCCUUGAGGGAAUGCCGUA Mycobacterium smegmatis (ATCC 10143) ssrA, internal partial SEQ ID NO: 202 ACTTCGAGCATCGAATCCAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCAACCAATTAAGCGCCGATT CCAATCAGCGCGACTACGCCCTCGCTGCCTAAGCGACGGCTG GTCTGTCAGACCGGGAGTGCCCTCGGCCCGGATCCTGGCATCA GCTAGAGGGACCCACCCACGGGTTCGGTCGCGGGACCTGTGG GGACATCAAACAGCGACTGGGATCGTCATCTCGGCTTGTTCGT GTGACCGGGAGATCCGAGTAGAGACATAGCGAACTGCGCACG GAGAAGCCTCGAGGACATGCCGTAG Mycobacterium smegmatis (ATCC 10143) ssrA, internal partial SEQ ID NO: 203 ACUUCGAGCAUCGAAUCCAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCAACCAAUUAAGCGCCGA UUCCAAUCAGCGCGACUACGCCCUCGCUGCCUAAGCGACGG CUGGUCUGUCAGACCGGGAGUGCCCUCGGCCCGGAUCCUGG CAUCAGCUAGAGGGACCCACCCACGGGUUCGGUCGCGGGAC CUGUGGGGACAUCAAACAGCGACUGGGAUCGUCAUCUCGGC UUGUUCGUGUGACCGGGAGAUCCGAGUAGAGACAUAGCGAA CUGCGCACGGAGAAGCCUCGAGGACAUGCCGUAG Mycobacterium xenopi (clinical isolate) ssrA, internal partial SEQ ID NO: 204 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCAACTAAATAAGCGCCGATT CACATCAGCGCGACTACGCTCTCGCTGCCTAAGCGACAGCTA GTCCGTCAGGCCGGGAGTTCCCTCGACCCGGATCCTGGCGTCA GCTAGAGGGATCCACCGATGGGTTCGGTCGCGGGACCCATCG GGACACCACACAGCGACTGGGATCGCCGTCCCGGCTAGTTCG CGAGACCGGGAGATCCGAGTAAGGGCAAAGCGAACTGCGCA CGGAGAAGCCTTGAGGGTATGCCGTA Mycobacterium xenopi (clinical isolate) tmRNA, internal partial SEQ ID NO: 205 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCAACUAAAUAAGCGCCGA UUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACAG CUAGUCCGUCAGGCCGGGAGUUCCCUCGACCCGGAUCCUGG CGUCAGCUAGAGGGAUCCACCGAUGGGUUCGGUCGCGGGAC CCAUCGGGACACCACACAGCGACUGGGAUCGCCGUCCCGGC UAGUUCGCGAGACCGGGAGAUCCGAGUAAGGGCAAAGCGAA CUGCGCACGGAGAAGCCUUGAGGGUAUGCCGUA Mycobacterium intracellulare (NCTC 10425) ssrA, internal partial SEQ ID NO: 206 ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA CCGACCACCGTAAGCGTCGTTGCAAACAGATAAGCGCCGATT CACATCAGCGCGACTACGCTCTCGCTGCCTAAGCGACAGCTA GTCCGTCAGACCGGGAACGCCCTCGACCCGGAGCCTGGCGTC AGCTAGAGGGATCCACCGATGAGTCCGGTCGCGGGACTTATC GGGACACCAACAGCGACTGGGATCGTCATCTCGGCTTGTTCGC GTGACCGGGAGATCCGAGTAGAGGCATAGCGAACTGCGCACG GAGAAGTCTTGAGGGAATGCCGTAG Mycobacterium intracellulare (NCTC 10425) tmRNA, internal partial SEQ ID NO: 207 ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA ACCGACCACCGUAAGCGUCGUUGCAAACAGAUAAGCGCCGA UUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACAG CUAGUCCGUCAGACCGGGAACGCCCUCGACCCGGAGCCUGG CGUCAGCUAGAGGGAUCCACCGAUGAGUCCGGUCGCGGGAC UUAUCGGGACACCAACAGCGACUGGGAUCGUCAUCUCGGCU UGUUCGCGUGACCGGGAGAUCCGAGUAGAGGCAUAGCGAAC UGCGCACGGAGAAGUCUUGAGGGAAUGCCGUAG Mycobacterium scrofulaceum (NCTC 10803) ssrA, internal partial SEQ ID NO: 208 ACATCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAA GAGACCACCGTAAGCGTCGTTGCAACCAATTAAGCGCCGATT CACATCAGCGCGACTACGCTCTCGCTGCCTAAGCGACAGCTA GTCCGTCAGACCGGGAAAGCCCTCGACCCGGAGCCTGGCGTC AGCTAGAGGGATCAACCGATGAGTTCGGTCGCGGGACTCATC GGGACACCAACAGCGACTGGGATCGTCATCCTGGCTAGTCCG CGTGACCAGGAGATCCGAGCAGAGGCATAGCGGACTGCGCAC GGAGAAGTCTTGAGGGAATGCCGTTG Mycobacterium scrofulaceum (NCTC 10803) tmRNA, internal partial SEQ ID NO: 209 ACAUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCA AGAGACCACCGUAAGCGUCGUUGCAACCAAUUAAGCGCCGA UUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACAG CUAGUCCGUCAGACCGGGAAAGCCCUCGACCCGGAGCCUGG CGUCAGCUAGAGGGAUCAACCGAUGAGUUCGGUCGCGGGAC UCAUCGGGACACCAACAGCGACUGGGAUCGUCAUCCUGGCU AGUCCGCGUGACCAGGAGAUCCGAGCAGAGGCAUAGCGGAC UGCGCACGGAGAAGUCUUGAGGGAAUGCCGUUG Nocardia asteroides ssrA, internal partial SEQ ID NO: 210 ACTGTGTGCGCCGAGGTAGGGGAAGCGTGTCGGTGCAGGCTG GAGACCACCGTTAAGCGTCGCGGCAACCAATTAAGCGCCGAT TCCAATCAGCGCGACTACGCCCTCGCTGCCTGATCAGCGACGG CTAGCTGTCGGCCCGGGTTGTGTTCCCGAACCCGGATGCCGGC ATCATCTCAGGGAACTCACCGTGTTCGCCGGTCGCGGACGGA CACGGGACAGCAAACAGCGACTGGGATCGTCATCTCGGCTTG TTCGCGTGACCGGGAGATCCAAGTAGAGACATAGCGGACTGC ACACGGAGAAGCCCTACTGACTCGACACAG Nocardia asteroides tmRNA, internal partial SEQ ID NO: 211 ACUGUGUGCGCCGAGGUAGGGGAAGCGUGUCGGUGCAGGCU GGAGACCACCGUUAAGCGUCGCGGCAACCAAUUAAGCGCCG AUUCCAAUCAGCGCGACUACGCCCUCGCUGCCUGAUCAGCG ACGGCUAGCUGUCGGCCCGGGUUGUGUUCCCGAACCCGGAU GCCGGCAUCAUCUCAGGGAACUCACCGUGUUCGCCGGUCGC GGACGGACACGGGACAGCAAACAGCGACUGGGAUCGUCAUC UCGGCUUGUUCGCGUGACCGGGAGAUCCAAGUAGAGACAUA GCGGCUGCACACGGAGAAGCCCUACUGACUCGACACAG Salmonella enteritidis ssrA, internal partial SEQ ID NO: 212 ACGGGATTTGCGAAACCCAAGGTGCATGCCGAGGGGCGGTTG GCCTCGTAAAAAGCCGCAAAAAAATAGTCGCAAACGACGAAA CCTACGCTTTAGCAGCTTAATAACCTGCTTAGAGCCCTCTCTC CCTAGCCTCCGCTCTTAGGACGGGGATCAAGAGAGGTCAAAC CCAAAAGAGATCGCGTGGATGCCCTGCCTGGGGTTGAAGCGT TAAAACGAATCAGGCTAGTCTGGTAGTGGCGTGTCCGTCCGC AGGTGCCAGGCGAATGTAAAGACTGACTAAGCATGTAGTACC GAGGATGTAGGAATTTCGG Salmonella enteritidis tmRNA, internal partial SEQ ID NO: 213 ACGGGAUUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUU GGCCUCGUAAAAAGCCGCAAAAAAAUAGUCGCAAACGACGA AACCUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUC UCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGU CAAACCCAAAAGAGAUCGCGUGGAUGCCCUGCCUGGGGUUG AAGCGUUAAAACGAAUCAGGCUAGUCUGGUAGUGGCGUGUC CGUCCGCAGGUGCCAGGCGAAUGUAAAGACUGACUAAGCAU GUAGUACCGAGGAUGUAGGAAUUUCGG Staphylococcus epidermidis (NCTC 11047) ssrA, internal partial SEQ ID NO: 214 ACAGGGGTCCCCCGAGCTTATTAAGCGTGTCGGAGGGTTGGC TCCGTCATCAACACATTTCGGTTAAATATAACTGACAAATCAA ACAATAATTTCGCAGTAGCTGCGTAATAGCCACTGCATCGCCT AACAGCATCTCCTACGTGCTGTTAACGCGATTCAACCCTAGTA GGATATGCTAAACACTGCCGCTTGAAGTCTGTTTAGATGAAAT ATAATCAAGCTAGTATCATGTTGGTTGTTTATTGCTTAGCATG ATGCGAAAATTATCAATAAACTACACACGTAGAAAGATTTGT ATCAGGACCTCTGG Staphylococcus epidermidis (NCTC 11047) tmRNA, internal partial SEQ ID NO: 215 ACAGGGGUCCCCCGAGCUUAUUAAGCGUGUCGGAGGGUUGG CUCCGUCAUCAACACAUUUCGGUUAAAUAUAACUGACAAAU CAAACAAUAAUUUCGCAGUAGCUGCGUAAUAGCCACUGCAU CGCCUAACAGCAUCUCCUACGUGCUGUUAACGCGAUUCAAC CCUAGUAGGAUAUGCUAAACACUGCCGCUUGAAGUCUGUUU AGAUGAAAUAUAAUCAAGCUAGUAUCAUGUUGGUUGUUUA UUGCUUAGCAUGAUGCGAAAAUUAUCAAUAAACUACACACG UAGAAAGAUUUGUAUCAGGACCUCUGG Streptococcus agalactiae (NCTC 8181) ssrA, internal partial SEQ ID NO: 216 ACAGGCATTATGAGGTATATTTTGCGACTCATCGGCAGATGTA AAATGCCAGTTAAATATAACTGCAAAAAATACAAATTCTTAC GCATTAGCTGCCTAAAAAACAGCCTGCGTGATCTTCACAAGAT TGTTTGCGTTTTGCTAGAAGGTCTTATTTATCAGCAAACTACG TTTGGCTACTGTCTAGTTAGTTAAAAAGAGATTTATAGACTCG CTATGTGAGGGCTTGAGTTATGTGTCATCACCTAGTTAAATCA ATACATAACCTATAGTTGTAGACAAATATATTAGCAGATGTTT GG Streptococcus agalactiae (NCTC 8181) tmRNA, internal partial SEQ ID NO: 217 ACAGGCAUUAUGAGGUAUAUUUUGCGACUCAUCGGCAGAUG UAAAAUGCCAGUUAAAUAUAACUGCAAAAAAUACAAAUUCU UACGCAUUAGCUGCCUAAAAAACAGCCUGCGUGAUCUUCAC AAGAUUGUUUGCGUUUUGCUAGAAGGUCUUAUUUAUCAGCA AACUACGUUUGGCUACUGUCUAGUUAGUUAAAAAGAGAUUU AUAGACUCGCUAUGUGAGGGCUUGAGUUAUGUGUCAUCACC UAGUUAAAUCAAUACAUAACCUAUAGUUGUAGACAAAUAUA UUAGCAGAUGUUUGG

Of the above sequences SEQ ID NOs 47 to 62, 65 to 68, 71 and 72, 98 and 99, 159 to 168 and 176-217 are novel sequences.

The above mentioned sequences can be used to form a database of ssrA gene sequences which can be used to identify a bacterial species, or for the generation of nucleic acid diagnostic assays.

Representative probes identified in accordance with the invention are as follows:

Salmonella:

1) Genius specific probe:

5′-CGAATCAGGCTAGTCTGGTAG-3′ SEQ ID NO: 218

Mycobacteria:

2) Oligonucleotide probe for detection of tuberculosis complex

TB01 SEQ ID NO: 219 5′-ACTCCTCGGACA (A/G) CCACAGCGA-3′ 3) Oligonucleotide probes for detection of M. avium and M. paratuberculosis sequences

Probe 1: SEQ ID NO: 220 PAV1-5′-GTTGCAAATAGATAAGCGCC-3′ Probe 2: SEQ ID NO: 221 PAV2-5′-TCCGTCAGCCCGGGAACGCC-3′

Listeria:

4) Oligonucleotide probe used in the determination of tmRNA integrity after heat killing treatment of cells:

LVtm: SEQ ID NO: 222 5′-TTTTGTTTTTCTTTGCCA-3′ Escherichia coli: 5) Oligonucleotide probe used in the determination of tmRNA integrity after heat killing treatment of cells:

Evtm: SEQ ID NO: 223 5′-AGTTTTCGTCGTTTGCGA-3′

Further representative primers identified in accordance with the invention are as follows:

Mycobacteria:

1) Degenerative oligonucleotide primers for the amplification of all mycobacterial sequences

5′ Primer SEQ ID NO: 224 10SAAM3-5′-CAGGCAA (G/C) (A/T/C) GACCACCGTAA-3′ 3′ Primer SEQ ID NO: 225 10SAAM4-5′ GGATCTCC(C/T)G(A/G)TC(A/T)C(A/G)CG (A/G)AC(A/T)A-3′ 2) Oligonucleotide primers for the amplification of M. avium and M. paratuberculosis

5′ Primer: SEQ ID NO: 226 AP1for-5′-TGCCGGTGCAGGCAACTG-3′ 3′ Primer: SEQ ID NO: 227 AP2rev-5′-CACGCGAACAAGCCAGGA-3′

BRIEF DESCRIPTION OF THE DRAWINGS

In the accompanying drawings:

FIG. 1 is a clustal alignment of E. coli and V. cholerae ssrA gene sequences;

FIG. 2 is a photograph of an agarose gel of total cellular RNA prepared from E. coli and V. cholerae cells;

FIG. 3 is a photograph of an autoradiogram of hybridisation of a V. cholerae oligonucleotide probe to tmRNA transcripts of E. coli and V. cholerae;

FIG. 4 is a photograph of an agarose gel of the amplified products of universal ssrA gene amplification primers from a panel of organisms;

FIG. 5 is a clustal alignment of the ssrA gene sequences from the Listeria species;

FIG. 6 is a clustal alignment of the L. monocytogenes and B. subtilus ssrA/tmRNA gene sequences;

FIG. 7 is a photograph of an agarose gel of the amplified products of Listeria genus specific PCR amplification primers from a panel of organisms;

FIG. 8 is a photograph of an autoradiogram of hybridised Listeria genus specific oligonucleotide probe to a panel of organisms as prepared in Example 4;

FIG. 9 is a photograph of an autoradiogram of hybridised L. monocytogenes species specific probe to a panel of organisms as prepared in Example 7;

FIG. 10 is a computer scanned image of a nylon membrane strip used in the multiple colorimetric probe detection of Listeria ssrA gene sequences as described in Example 6.

FIG. 11 is a clustal alignment of ssrA gene sequences from C. trachomatis strains;

FIG. 12 is a clustal alignment of ssrA gene sequences from H. pylori strains;

FIG. 13 is a clustal alignment of ssrA gene sequences from M. genitalium strains;

FIG. 14 is a clustal alignment of ssrA gene sequences from N. gonorrhoeae strains;

FIG. 15 is a clustal alignment of ssrA gene sequences from L. monocytogenes strains;

FIG. 16 is a clustal alignment of ssrA gene sequences from L. monocytogenes strains and the L. innocua strain;

FIG. 17 is a photograph of an autoradiogram hybridised Listeria oligonucleotide probe (Evtm) to total RNA samples isolated after medium heat treatment of E. coli cells;

FIG. 18 is a photograph of an autoradiogram hybridised Listeria oligonucleotide probe (Evtm) to total RNA samples isolated after extreme heat treatment of E. coli cells;

FIG. 19 is a photograph of an autoradiogram hybridised Listeria oligonucleotide probe (Lvtm) to total RNA samples isolated after medium heat treatment of L. monocytogenes cells;

FIG. 20 is a photograph of an autoradiogram hybridised Listeria oligonucleotide probe (Lvtm) to total RNA samples isolated after extreme heat treatment of L. monocytogenes cells; and

FIG. 21 is a photograph of an agarose gel of RT-PCR generated tmRNA products at various time points post heat treatment.

The invention will be further illustrated by the following Examples.

MODES FOR CARRYING OUT THE INVENTION Example 1 Examination of the Primary Nucleotide Sequences of Available tmRNA Sequences

A comparative primary nucleotide sequence alignment of available tmRNA sequences using the Clustal W nucleic acid alignment programme demonstrated that tmRNA sequences from prokaryotes show a more significant degree of nucleotide sequence variability and non-homology than other bacterial high copy number RNA, as demonstrated in Table 1.

TABLE 1 Percentage nucleotide sequence homology between RNA molecules from different bacteria. Bacillus subtilus vs. Escherichia coli vs. Mycobacterium Vibrio cholerae tuberculosis rRNA % homology 88 66 tmRNA % homology 68 25

These regions of non-homology between tmRNA sequences from different bacteria are located in the middle of the molecule, and the extent of nucleotide sequence non-homology within the tmRNA molecule indicated that genus as well as species specific probes could be generated to distinguish between and/or detect bacteria.

Nucleotide sequence alignments had previously shown that the 5′ and 3′ flanking regions of the tmRNA molecules share a high degree of homology both within species and within genus. This observation indicated that universal oligonucleotide primers could be generated to amplify the ssrA gene or its encoding tmRNA from a wide variety of bacteria.

We have now demonstrated that these regions of homology and non-homology within the nucleotide sequence of tmRNA molecules from different organisms can be used as the basis of identifying and detecting organisms at the molecular level.

Example 2 Development of a V. cholerae tmRNA Specific Probe

A nucleotide sequence alignment of the E. coli (SEQ ID NO. 37) and V. cholerae (SEQ ID NO. 127) ssrA sequences as depicted in FIG. 1, shows that these two bacterial species are phylogenetically closely related. There are however, regions of non-homology between the sequences as evidenced by the absence of asterix marks. An oligonucleotide probe, complementary to the variable region of the V. cholerae ssrA nucleotide sequence underlined in FIG. 1, was synthesised.

The sequence of the V. cholerae tmRNA specific probe is

5′-AACGAATGGCTAACCTGAA-3′ SEQ ID NO. 169

Total RNA was isolated from liquid cultures of E. coli and V. cholerae at the mid-exponential phase and the stationary phase of growth. Equivalent amounts of the isolated total RNA were electrophoresed on a denaturing formaldehyde agarose gel and blotted onto HYBOND-N nylon membrane as shown in FIG. 2 in which the Lanes 1-4 represent the following:

Lane 1: Total E. coli RNA mid-log phase Lane 2: Total V. cholerae RNA mid-log phase Lane 3: Total E. coli RNA stationary phase Lane 4: Total V. cholerae RNA stationary phase

The resulting Northern blot was then hybridised with the V. cholerae tmRNA specific probe end-labelled with γP³². The results of the hybridisation experiment shown in FIG. 3 demonstrate the specificity of the probe as only V. cholerae tmRNAs were detected. Moreover, a greater degree of hybridisation signal intensity was observed with the V. cholerae tmRNA isolated from cultures during the stationary phase of growth, indicating that a higher copy number of the tmRNA molecule is present in V. cholerae cells during this phase.

Example 3 Generation of Universal ssrA/tmRNA Oligonucleotide Amplification Primers for the Characterisation of Unknown ssrA Gene and tmRNA Sequences

Clustal W alignment of all available ssrA gene and tmRNA sequences indicated that degenerate oligonucleotide primers could be designed to amplify ssrA gene and tmRNA nucleotide sequences for a wide variety of organisms.

Degenerate oligonucleotide primers were synthesised to PCR amplify ssrA gene sequences from total genomic DNA preparations from a broad range of bacteria.

The sequences of the synthesised degenerate oligonucleotides are as follows:

(a) tmU5′: 5′ in vitro PCR amplification primer SEQ ID NO: 170 5′-GGG(A/C)(C/T)TACGG(A/T)TTCGAC-3′ (b) tmU3′: 3′ in vitro PCR amplification primer SEQ ID NO: 171 5′-GGGA(A/G)TCGAACC(A/G)(C/G)GTCC-3′

-   -   Degenerate base positions are in parentheses.

The products of PCR reactions were electrophoresed on an agarose gel and a 350 base pair (approx.) PCR product was amplified in all cases, as shown in FIG. 4, demonstrating the “universality” of the degenerate tmRNA primers.

In FIG. 4 the lanes represent the following:

Lane A: Molecular weight marker V Lane 1: Escherichia coli Lane 2: Salmonella poona Lane 3: Klebsiella aerogenes Lane 4: Proteus mirabilis Lane 5: Proteus rettgeri Lane 6: Aeromonas hydrophilia Lane 7: Staphyloccus aureus Lane 8: Enterococcus faecalis Lane 9: Lactobacillus lactis Lane 10: Bacillus subtilus Lane 11: Listeria monocytogenes Lane 12: Listeria innocua Lane 13: Listeria murrayi Lane 14: Listeria welshimeri Lane 15: Listeria grayi Lane 16: Mycobacterium bovis Lane B: Molecular weight marker V

The universal primers amplified the ssrA gene from both Gram positive and Gram negative bacteria, as shown in Table 2.

TABLE 2 Bacterial species tested with universal amplification primers. PCR Product Gram negative bacteria Escherichia coli + Salmonella poona + Klebsiella aerogenes + Proteus mirabilis + Proteus rettgeri + Aeromonas hydrophilia + Gram positive bacteria Staphyloccus aureus + Enterococcus faecalis + Lactobacillus lactis + Bacillus subtilus + Listeria monocytogenes + Listeria innocua + Listeria murrayi + Listeria welshimeri + Listeria grayi + Mycobacterium bovis +

Example 4 Isolation and Characterisation of Previously Unknown Bacterial ssrA/tmRNA Nucleotide Sequences

The PCR products amplified from genomic DNA from the Listeria species of bacteria and that from the M. bovis bacterium, from Example 2, were subcloned into a T-tailed plasmid vector for the purposes of DNA sequencing. Three recombinant clones were selected for each species and sequenced by the di-deoxy sequencing method. The sequence of both DNA strands for each subclone was determined.

The nucleotide sequence determined for the M. bovis ssrA gene shared 100% homology with the Mycobacterium tuberculosis ssrA gene sequence.

A clustal W alignment of the novel ssrA gene sequences obtained for the Listeria species (SEQ ID NOS 51, 53, 55, 59 and 61) is shown in FIG. 5. This analysis indicated that genus-specific probes and oligonucleotide amplification primers can be generated for Listeria bacteria. Furthermore, the alignment also indicated that a species specific oligonucleotide probe can be generated which will distinguish L. monocytogenes from the other Listeria species.

In FIG. 5 the proposed genus specific oligonucleotide primers, Ltm 1 and Ltm 2, are boxed, as is the genus specific Listeria oligonucleotide probe, LGtm. The proposed L. monocytogenes species specific oligonucleotide probe sequence, LStm, is underlined and italicised.

To further illustrate that the ssrA gene/tmRNA nucleic acid target is a suitable target for bacterial diagnostics, a comparative alignment of the L. monocytogenes ssrA gene nucleotide sequence (SEQ ID NO. 55) with the available B. subtilis ssrA gene nucleotide sequence (SEQ ID NO. 11) (a phylogenetically closely related bacteria to Listeria) was carried out as shown in FIG. 6. Analysis of the sequence alignment showed a percentage nucleotide sequence homology of 41%, whereas the corresponding 16S rRNA alignment exhibits a nucleotide sequence percentage homology of 87%, (data not shown).

Example 5 Generation and Application of ssrA Gene/tmRNA Genus-Specific Amplification Primers, Genus-Specific and Species-Specific Probes for the Listeria Bacterial Species

Using the Listeria genus ssrA gene/tmRNA nucleotide sequence alignment of Example 4, regions of the ssrA gene/tmRNA nucleotide sequence were analysed to determine their suitability for the generation of genus-specific amplification primers, and genus-specific and species-specific oligonucleotide probes. In this analysis, regions which demonstrated the greatest sequence differences to B. subtilis, were selected in the design of these amplification primers and probes.

The sequences of the synthesised oligonucleotides are as follows:

(a) Ltm1: 5′ Listeria genus specific amplification primer SEQ ID NO: 172 5′-AAAGCCAATAATAACTGG-3′ (b) Ltm2: 3′ Listeria genus specific amplification primer SEQ ID NO: 173 5′-CCAGAAATATCGGCACTT-3′ (c) LGtm: Listeria genus specific hybridisation probe SEQ ID NO: 174 5′-GTGAGACCCTTACCGTAG-3′ (d) LStm: L. monocytogenes species specific hybridisation probe SEQ ID NO: 175 5′-TCTATTTAACCCCAGACG-3′

The genus specific amplification primers Ltm1 and Ltm2 were used in a series of PCR reactions with total genomic DNA from twenty different strains as the template in each case. Only ssrA gene sequences from the Listeria species were amplified (260 base pair product) with these primers (FIG. 7 and Table 3) demonstrating that the ssrA gene/tmRNA is a suitable target for specific in vitro amplification of a bacterial genus. No amplification products were observed for any other bacterial species tested, although PCR products were obtained from the DNA from these bacterial species using the universal primers (tmU5′ and tmU3′) described in Example 2.

In FIG. 7 the lanes represent the following:

Lane A: Molecular weight marker V Lane 1: E. coli Lane 2: S. poona Lane 3: K. aerogenes Lane 4: P. mirabilis Lane 5: P. rettgeri Lane 6: A. hydrophilia Lane 7: S. aureus Lane 8: E. faecalis Lane 9: L. lactis Lane 10: B. subtilus Lane 11: L. monocytogenes strain 1 Lane 12: L. monocytogenes strain 2 Lane 13: L. monocytogenes strain 3 Lane 14: L. monocytogenes strain 4 Lane 15: L. monocytogenes clinical isolate Lane 16: L. innocua Lane 17: L. murrayi Lane 18: L. welshimeri Lane 19: L. grayi Lane 20: M. bovis Lane B: Molecular weight marker V

TABLE 3 Bacterial species tested with Listeria specific amplification primers. PCR Product Gram negative Escherichia coli − bacteria Salmonella poona − Klebsiella aerogenes − Proteus mirabilis − Proteus rettgeri − Aeromonas hydrophilia − Gram positive Staphyloccus aureus − bacteria Entrococcus faecalis − Lactobacillus lactis − Bacillus subtilus − Listeria monocytogenes strain 1 + Listeria monocytogenes strain 2 + Listeria monocytogenes strain 3 + Listeria monocytogenes strain 4 + Listeria monocytogenes clinical + isolate Listeria innocua + Listeria murrayi + Listeria welshimeri + Listeria grayi + Mycobacterium bovis −

The Listeria genus specific oligonucleotide probe, LGtm, was hybridised to the Southern blot depicted in FIG. 4. Positive hybridisation signals were observed only with Listeria species as shown in FIG. 8 and Table 4, demonstrating the utility of the tmRNA sequence as a target in detecting a specific genus.

In FIG. 8 the lanes represent the following:

Lane A: Molecular weight marker V Lane 1: Escherichia coli Lane 2: Salmonella poona Lane 3: Klebsiella aerogenes Lane 4: Proteus mirabilis Lane 5: Proteus rettgeri Lane 6: Aeromonas hydrophilia Lane 7: Staphyloccus aureus Lane 8: Enterococcus faecalis Lane 9: Lactobacillus lactis Lane 10: Bacillus subtilus Lane 11: Listeria monocytogenes Lane 12: Listeria innocua Lane 13: Listeria murrayi Lane 14: Listeria welshimeri Lane 15: Listeria grayi Lane 16: Mycobacterium bovis Lane B: Molecular weight marker V

The PCR products generated using the genus-specific amplification described in this Example, and shown in FIG. 7, were Southern blotted and hybridised to the L. monocytogenes species-specific oligonucleotide probe. A positive hybridisation signal was observed with three of the four typed strains and the clinical isolate of L. monocytogenes as shown in FIG. 9 and Table 4.

In FIG. 9 the lanes represent the following:

Lane A: Molecular weight marker V Lane 1: E. coli Lane 2: S. poona Lane 3: K. aerogenes Lane 4: P. mirabilis Lane 5: P. rettgeri Lane 6: A. hydrophilia Lane 7: S. aureus Lane 8: E. faecalis Lane 9: L. lactis Lane 10: B. subtilus Lane 11: L. monocytogenes strain 1 Lane 12: L. monocytogenes strain 2 Lane 13: L. monocytogenes strain 3 Lane 14: L. monocytogenes strain 4 Lane 15: L. monocytogenes clinical isolate Lane 16: L. innocua Lane 17: L. murrayi Lane 18: L. welshimeri Lane 19: L. grayi Lane 20: M. bovis Lane B: Molecular weight marker V

TABLE 4 Specificity of the Listeria genus-specific probe and the L. monocytogenes species-specific probe. LGtm LStm Genus- Species- specific specific probe probe Gram negative Escherichia coli − − bacteria Salmonella poona − − Klebsiella aerogenes − − Proteus mirabilis − − Proteus rettgeri − − Aeromonas hydrophilia − − Gram positive Staphyloccus aureus − − bacteria Entrococcus faecalis − − Lactobacillus lactis − − Bacillus subtilus − − Listeria monocytogenes strain 1 + + Listeria monocytogenes strain 2 + + Listeria monocytogenes strain 3 + + Listeria monocytogenes strain 4 + − Listeria monocytogenes + + clinical isolate Listeria innocua + − Listeria murrayi + − Listeria welshimeri + − Listeria grayi + − Mycobacterium bovis − −

One of the typed L. monocytogenes strains, strain 4, failed to generate a positive signal with this probe. DNA sequencing of the PCR amplified ssrA gene from this strain demonstrated that it contained a probe target region identical to L. innocua. It should be noted however that the ssrA gene from this strain contains other regions where the sequence is identical to the previously characterised L. monocytogenes strain and that these sequences are different to the L. innocua sequence, as shown in FIG. 15. Therefore a species specific oligonucleotide directed to one of these variable regions can be synthesised which would recognise each strain type (isolate) within the species, for example L. monocytogenes.

Example 6 Multiple Colorimetric Probe Detection of Listeria ssrA Gene Sequences

LGTm (A), LStm (B) and a Campylobacter upsaliensis 16S-23S rRNA spacer (C-5′ CATTAAACTTTAGCAAGGAAGTG 3′) SEQ ID NO: 228 oligonucleotide probe were irreversibly bound to nylon membrane strips and hybridised to with amplified ssrA PCR product, using the genus specific primers Ltm1 and Ltm2 (Ltm1 was labelled with biotin at the 5′ end), from L. monocytogenes (1-6), L. innocua (7-10), L. ivanovii (11), L. murrayi (12), L. seeligeri (13), L. welshmeri (14) and L. grayii (15). The ssrA amplified PCR products, using tmU5′ and tmU3′ (tmU5′ was labelled with biotin at the 5′ end), were also hybridised to the nylon membrane strips from the Gram-positive bacteria, B. subtilus, L. lactis, S. aureus, S. epidermis, E. faecalis, C. perfringins (16-21) and the Gram-negative bacteria E. coli, S. enteritidis, P. Rettgeri, K. aerogenes (22-25). As shown in FIG. 10 after hybridisation, development of the colorimetric assay to biotin revealed the following: Strips 1-6 demonstrates that the ssrA amplified PCR product originated from L. monocytogenes combined with the confirmation that the PCR product amplified is from the genus Listeria—A and B give colour detection; Strips 7-15 demonstrate that these PCR products originated from the genus Listeria—only A gives colour detection; and Strips 16-25 demonstrate that the PCR products are not from the genus Listeria—no colour detection. C is a negative oligonucleotide control probe and D is a positive control colorimetric detection assay for all samples.

Example 7 Use of ssrA/tmRNA Sequences to Distinguish Between Species of Organisms

Clustal W alignments as shown in FIGS. 11 (SEQ ID NOS. 19 and 21), 12 (SEQ ID NOS. 41 and 43), 13 (SEQ ID NOS. 77 and 79), 14 (SEQ ID NOS. 83 and 85), 15 and 16 (SEQ ID NO. 53, 55 and 57), indicate that there are nucleotide differences within the ssrA/tmRNA sequences of different strains of the same bacteria. This suggests that the ssrA/tmRNA sequences could potentially be used to discriminate between individual and/or groups of strains within a bacterial species. This may have useful applications in epidemiology and bacterial population analysis.

Example 8 tmRNA Integrity Analysis after Medium and Extreme Heat Treatment of Bacterial Cells

E. coli and L. monocytogenes cultures were heat treated at 80° C., for 20 min. in the case of E. coli and 40 min. in the case of L. monocytogenes and at 120° C. for 15 min. (autoclaving) after overnight growth and

-   -   tested for viability at 0 h, 1 h, 2 h, 6 h, 12 h, 24 h and 48 h         after heat treatment. No viability was observed at each time         period tested. Total RNA was also isolated at these time periods         and electrophoresed on

denaturing 1.2% agarose gels and Northern blotted. Each blot was hybridised to, in the case of E. coli (FIGS. 17 and 18) with a radioactively labelled oligonucleotide probe Evtm and in the case of L. monocytogenes (FIGS. 19 and 20) with a radiolabelled LVtm. No tmRNA transcript was detected with each sample tested, demonstrating that tmRNA transcript is degraded after heat treatment. The lanes represented with the notation

-   -   +ve is a positive control total RNA sample.

Example 9 Use of the tmRNA Transcript in Distinguishing Between Viable and Non-Viable Bacteria

A 100 ml culture of L. monocytogenes was grown overnight in liquid culture. After growth, serial dilutions of the cells were carried out and viability was determined by spread plating on nutrient agar plates. Simultaneously, total RNA was isolated from a 1 ml aliquot of these cells. The remainder of the cells were heated at 65° C. for 20 min. Cells were then removed for both viability analysis and total RNA isolation. Samples were taken for viability and RNA isolation at time periods of 0 h, 2 h, 6 h and 24 h after treatment.

Spread plating on nutrient agar plates indicated that heat treatment killed L. monocytogenes cells, with no viable colony forming units observed. Each RNA sample isolated was then treated with DNase to remove any contaminating DNA and total RNA samples (100 ng) were subjected to Reverse Transcriptase-PCR amplification using the Listeria genus specific ssrA/tmRNA oligonucleotide primers Ltm1 and Ltm2. Negative control amplification reactions included primers, target, and Taq polymerase, but no Reverse Transcriptase. The results of the amplification reactions are shown in FIG. 12.

Amplified tmRNA RT-PCR products were only observed with the RNA sample which was not heat treated. All other samples gave no RT-PCR product indicating that the tmRNA molecules in these samples may have been degraded in the non-viable heat treated cells.

In FIG. 21 the lanes represent the following:

Lane A: Molecular weight marker V; Lane 1: PCR amplification of RNA (no heat treatment of cells)

-   -   −Reverse Transcriptase (RT), +Taq polymerase (TP);         Lane 2: RT-PCR of RNA (no heat treatment of cells), +RT, +TP;         Lane 3: PCR amplification of RNA (at 0 time after heat         treatment),     -   −RT, +TP;         Lane 4: RT-PCR of RNA (at 0 time after heat treatment), +RT,         +TP;         Lane 5: PCR amplification of RNA (at 1 h time after heat         treatment),     -   −RT, +TP;         Lane 6: RT-PCR of RNA (at 1 h time after heat treatment),     -   +RT, +TP;         Lane 7: PCR amplification of RNA (at 2 h time after heat         treatment),     -   −RT, +TP;         Lane 8: RT-PCR of RNA (at 2 h time after heat treatment), +RT,         +TP;         Lane 9: PCR amplification of RNA (at 6 h time after heat         treatment), −RT, +TP;         Lane 10: RT-PCR of RNA (at 6 h time after heat treatment), +RT,         +TP;         Lane 11: PCR amplification of RNA (at 24 h time after heat         treatment),     -   −RT, +TP;         Lane 12: RT-PCR of RNA (at 24 h time after heat treatment),     -   +RT, +TP;         Lane B: Molecular weight marker V. 

1-29. (canceled)
 30. An isolated nucleic acid sequence selected from the group consisting of the tmRNA sequence for Chlamydia trachomatis set forth in SEQ ID NO:20, a DNA sequence encoding said tmRNA sequence, and a complement of said DNA sequence.
 31. An isolated nucleic acid sequence according to claim 30, wherein said DNA sequence is the ssrA gene as set forth in SEQ ID NO:19.
 32. A method for diagnosing a bacterial infectious agent comprising determining the presence of a bacterial nucleic acid sequence selected from the group consisting of the tmRNA sequence for Chlamydia trachomatis set forth in SEQ ID NO:20, a DNA sequence encoding said tmRNA sequence, and a complement of said DNA sequence.
 33. A method according to claim 32, wherein said DNA sequence is the ssrA gene as set forth in SEQ ID NO:19.
 34. The method of claim 32, wherein the determination is made by performing an amplification-based assay.
 35. The isolated nucleic acid sequence of claim 30, wherein the nucleic acid sequence is the DNA sequence encoding the tmRNA sequence for Chlamydia trachomatis set forth in SEQ ID NO:20.
 36. The method of claim 32, wherein the bacterial nucleic acid sequence is the DNA sequence encoding the tmRNA sequence for Chlamydia trachomatis set forth in SEQ ID NO:20.
 37. The method of claim 34, wherein the bacterial nucleic acid sequence is the DNA sequence encoding the tmRNA sequence for Chlamydia trachomatis set forth in SEQ ID NO:20. 